<?xml version="1.0" encoding="UTF-8"?>

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2024 Workiva-->
<!--r:72729ecf-7e7a-467c-900d-d84b77f77c86,g:cf4d12ad-5c0e-490d-9b37-fca127307435-->
<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:jkhy="http://www.jackhenry.com/20240630" xmlns:xbrli="http://www.xbrl.org/2003/instance" xmlns:dtr-types1="http://www.xbrl.org/dtr/type/2020-01-21" xmlns:dtr-types="http://www.xbrl.org/dtr/type/2022-03-31" attributeFormDefault="unqualified" elementFormDefault="qualified" targetNamespace="http://www.jackhenry.com/20240630">
  <xs:import namespace="http://fasb.org/srt/2024" schemaLocation="https://xbrl.fasb.org/srt/2024/elts/srt-2024.xsd"/>
  <xs:import namespace="http://fasb.org/us-gaap/2024" schemaLocation="https://xbrl.fasb.org/us-gaap/2024/elts/us-gaap-2024.xsd"/>
  <xs:import namespace="http://www.w3.org/1999/xlink" schemaLocation="http://www.xbrl.org/2003/xlink-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/instance" schemaLocation="http://www.xbrl.org/2003/xbrl-instance-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/2003/linkbase" schemaLocation="http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd"/>
  <xs:import namespace="http://www.xbrl.org/dtr/type/2020-01-21" schemaLocation="https://www.xbrl.org/dtr/type/2020-01-21/types.xsd"/>
  <xs:import namespace="http://www.xbrl.org/dtr/type/2022-03-31" schemaLocation="https://www.xbrl.org/dtr/type/2022-03-31/types.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/dei/2024" schemaLocation="https://xbrl.sec.gov/dei/2024/dei-2024.xsd"/>
  <xs:import namespace="http://xbrl.sec.gov/ecd/2024" schemaLocation="https://xbrl.sec.gov/ecd/2024/ecd-2024.xsd"/>
  <xs:annotation>
    <xs:appinfo>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20240630_pre.xml" xlink:role="http://www.xbrl.org/2003/role/presentationLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20240630_def.xml" xlink:role="http://www.xbrl.org/2003/role/definitionLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20240630_lab.xml" xlink:role="http://www.xbrl.org/2003/role/labelLinkbaseRef" xlink:type="simple"/>
      <link:linkbaseRef xmlns:xlink="http://www.w3.org/1999/xlink" xlink:arcrole="http://www.w3.org/1999/xlink/properties/linkbase" xlink:href="jkhy-20240630_cal.xml" xlink:role="http://www.xbrl.org/2003/role/calculationLinkbaseRef" xlink:type="simple"/>
      <link:roleType id="CoverPage" roleURI="http://www.jackhenry.com/role/CoverPage">
        <link:definition>0000001 - Document - Cover Page</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONSOLIDATEDSTATEMENTSOFINCOME" roleURI="http://www.jackhenry.com/role/CONSOLIDATEDSTATEMENTSOFINCOME">
        <link:definition>9952151 - Statement - CONSOLIDATED STATEMENTS OF INCOME</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONSOLIDATEDBALANCESHEETS" roleURI="http://www.jackhenry.com/role/CONSOLIDATEDBALANCESHEETS">
        <link:definition>9952152 - Statement - CONSOLIDATED BALANCE SHEETS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONSOLIDATEDSTATEMENTSOFCHANGESINSTOCKHOLDERSEQUITY" roleURI="http://www.jackhenry.com/role/CONSOLIDATEDSTATEMENTSOFCHANGESINSTOCKHOLDERSEQUITY">
        <link:definition>9952153 - Statement - CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="CONSOLIDATEDSTATEMENTSOFCASHFLOWS" roleURI="http://www.jackhenry.com/role/CONSOLIDATEDSTATEMENTSOFCASHFLOWS">
        <link:definition>9952154 - Statement - CONSOLIDATED STATEMENTS OF CASH FLOWS</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NatureofOperationsandSummaryofSignificantAccountingPoliciesTextBlock" roleURI="http://www.jackhenry.com/role/NatureofOperationsandSummaryofSignificantAccountingPoliciesTextBlock">
        <link:definition>9952155 - Disclosure - Nature of Operations and Summary of Significant Accounting Policies (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenueandDeferredCosts" roleURI="http://www.jackhenry.com/role/RevenueandDeferredCosts">
        <link:definition>9952156 - Disclosure - Revenue and Deferred Costs</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairValueMeasuresandDisclosures" roleURI="http://www.jackhenry.com/role/FairValueMeasuresandDisclosures">
        <link:definition>9952157 - Disclosure - Fair Value Measures and Disclosures</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="Leases" roleURI="http://www.jackhenry.com/role/Leases">
        <link:definition>9952158 - Disclosure - Leases</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="PropertyandEquipmentTextBlock" roleURI="http://www.jackhenry.com/role/PropertyandEquipmentTextBlock">
        <link:definition>9952159 - Disclosure - Property and Equipment (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OtherAssetsTextBlock" roleURI="http://www.jackhenry.com/role/OtherAssetsTextBlock">
        <link:definition>9952160 - Disclosure - Other Assets (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DebtTextBlock" roleURI="http://www.jackhenry.com/role/DebtTextBlock">
        <link:definition>9952161 - Disclosure - Debt (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncomeTaxesTextBlock" roleURI="http://www.jackhenry.com/role/IncomeTaxesTextBlock">
        <link:definition>9952162 - Disclosure - Income Taxes (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndustryandSupplierConcentrationsTextBlock" roleURI="http://www.jackhenry.com/role/IndustryandSupplierConcentrationsTextBlock">
        <link:definition>9952163 - Disclosure - Industry and Supplier Concentrations (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockBasedCompensationTextBlock" roleURI="http://www.jackhenry.com/role/StockBasedCompensationTextBlock">
        <link:definition>9952164 - Disclosure - Stock Based Compensation (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EarningsPerShareTextBlock" roleURI="http://www.jackhenry.com/role/EarningsPerShareTextBlock">
        <link:definition>9952165 - Disclosure - Earnings Per Share (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EmployeeBenefitPlansTextBlock" roleURI="http://www.jackhenry.com/role/EmployeeBenefitPlansTextBlock">
        <link:definition>9952166 - Disclosure - Employee Benefit Plans (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinessAcquisitionsTextBlock" roleURI="http://www.jackhenry.com/role/BusinessAcquisitionsTextBlock">
        <link:definition>9952167 - Disclosure - Business Acquisitions (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ReportableSegmentInformationTextBlock" roleURI="http://www.jackhenry.com/role/ReportableSegmentInformationTextBlock">
        <link:definition>9952168 - Disclosure - Reportable Segment Information (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SubsequentEventsTextBlock" roleURI="http://www.jackhenry.com/role/SubsequentEventsTextBlock">
        <link:definition>9952169 - Disclosure - Subsequent Events (Text Block)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NatureofOperationsandSummaryofSignificantAccountingPoliciesPolicies" roleURI="http://www.jackhenry.com/role/NatureofOperationsandSummaryofSignificantAccountingPoliciesPolicies">
        <link:definition>9954471 - Disclosure - Nature of Operations and Summary of Significant Accounting Policies (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairValueMeasuresandDisclosuresPolicies" roleURI="http://www.jackhenry.com/role/FairValueMeasuresandDisclosuresPolicies">
        <link:definition>9954472 - Disclosure - Fair Value Measures and Disclosures (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesPolicies" roleURI="http://www.jackhenry.com/role/LeasesPolicies">
        <link:definition>9954473 - Disclosure - Leases (Policies)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OrganizationConsolidationandPresentationofFinancialStatementsTables" roleURI="http://www.jackhenry.com/role/OrganizationConsolidationandPresentationofFinancialStatementsTables">
        <link:definition>9954474 - Disclosure - Organization, Consolidation and Presentation of Financial Statements (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenuefromContractwithCustomerTables" roleURI="http://www.jackhenry.com/role/RevenuefromContractwithCustomerTables">
        <link:definition>9954475 - Disclosure - Revenue from Contract with Customer (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairValueMeasuresandDisclosuresTables" roleURI="http://www.jackhenry.com/role/FairValueMeasuresandDisclosuresTables">
        <link:definition>9954476 - Disclosure - Fair Value Measures and Disclosures (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesTables" roleURI="http://www.jackhenry.com/role/LeasesTables">
        <link:definition>9954477 - Disclosure - Leases (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="PropertyandEquipmentTables" roleURI="http://www.jackhenry.com/role/PropertyandEquipmentTables">
        <link:definition>9954478 - Disclosure - Property and Equipment (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OtherAssetsTables" roleURI="http://www.jackhenry.com/role/OtherAssetsTables">
        <link:definition>9954479 - Disclosure - Other Assets (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncomeTaxesIncomeTaxesTables" roleURI="http://www.jackhenry.com/role/IncomeTaxesIncomeTaxesTables">
        <link:definition>9954480 - Disclosure - Income Taxes Income Taxes (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockBasedCompensationTables" roleURI="http://www.jackhenry.com/role/StockBasedCompensationTables">
        <link:definition>9954481 - Disclosure - Stock Based Compensation (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EarningsPerShareTables" roleURI="http://www.jackhenry.com/role/EarningsPerShareTables">
        <link:definition>9954482 - Disclosure - Earnings Per Share (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ReportableSegmentInformationTables" roleURI="http://www.jackhenry.com/role/ReportableSegmentInformationTables">
        <link:definition>9954483 - Disclosure - Reportable Segment Information (Tables)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NatureofOperationsandSummaryofSignificantAccountingPoliciesDetails" roleURI="http://www.jackhenry.com/role/NatureofOperationsandSummaryofSignificantAccountingPoliciesDetails">
        <link:definition>9954484 - Disclosure - Nature of Operations and Summary of Significant Accounting Policies (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NatureofOperationsandSummaryofSignificantAccountingPoliciesAllowanceforCreditLossesDetails" roleURI="http://www.jackhenry.com/role/NatureofOperationsandSummaryofSignificantAccountingPoliciesAllowanceforCreditLossesDetails">
        <link:definition>9954485 - Disclosure - Nature of Operations and Summary of Significant Accounting Policies Allowance for Credit Losses (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="NatureofOperationsandSummaryofSignificantAccountingPoliciesPurchaseofInvestmentDetails" roleURI="http://www.jackhenry.com/role/NatureofOperationsandSummaryofSignificantAccountingPoliciesPurchaseofInvestmentDetails">
        <link:definition>9954486 - Disclosure - Nature of Operations and Summary of Significant Accounting Policies Purchase of Investment (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ReportableSegmentInformationDetails" roleURI="http://www.jackhenry.com/role/ReportableSegmentInformationDetails">
        <link:definition>9954487 - Disclosure - Reportable Segment Information (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="TreasuryStockDetails" roleURI="http://www.jackhenry.com/role/TreasuryStockDetails">
        <link:definition>9954488 - Disclosure - Treasury Stock (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DisaggregationofRevenueDetails" roleURI="http://www.jackhenry.com/role/DisaggregationofRevenueDetails">
        <link:definition>9954489 - Disclosure - Disaggregation of Revenue (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenueandDeferredCostsContractBalancesDetails" roleURI="http://www.jackhenry.com/role/RevenueandDeferredCostsContractBalancesDetails">
        <link:definition>9954490 - Disclosure - Revenue and Deferred Costs Contract Balances (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenueandDeferredCostsNarrativeDetails" roleURI="http://www.jackhenry.com/role/RevenueandDeferredCostsNarrativeDetails">
        <link:definition>9954491 - Disclosure - Revenue and Deferred Costs Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenueandDeferredCostsNarrativeDetails_1" roleURI="http://www.jackhenry.com/role/RevenueandDeferredCostsNarrativeDetails_1">
        <link:definition>9954491 - Disclosure - Revenue and Deferred Costs Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="RevenueandDeferredCostsContractCostsDetails" roleURI="http://www.jackhenry.com/role/RevenueandDeferredCostsContractCostsDetails">
        <link:definition>9954492 - Disclosure - Revenue and Deferred Costs Contract Costs (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="FairValueMeasuresandDisclosuresDetails" roleURI="http://www.jackhenry.com/role/FairValueMeasuresandDisclosuresDetails">
        <link:definition>9954493 - Disclosure - Fair Value Measures and Disclosures (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesDetails" roleURI="http://www.jackhenry.com/role/LeasesDetails">
        <link:definition>9954494 - Disclosure - Leases (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesLeaseMaturityDetails" roleURI="http://www.jackhenry.com/role/LeasesLeaseMaturityDetails">
        <link:definition>9954495 - Disclosure - Leases Lease Maturity (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="LeasesLeaseMaturityDetails_1" roleURI="http://www.jackhenry.com/role/LeasesLeaseMaturityDetails_1">
        <link:definition>9954495 - Disclosure - Leases Lease Maturity (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="PropertyandEquipmentDetails" roleURI="http://www.jackhenry.com/role/PropertyandEquipmentDetails">
        <link:definition>9954496 - Disclosure - Property and Equipment (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OtherAssetsGoodwillDetails" roleURI="http://www.jackhenry.com/role/OtherAssetsGoodwillDetails">
        <link:definition>9954497 - Disclosure - Other Assets Goodwill (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OtherAssetsOtherIntangibleAssetsDetails" roleURI="http://www.jackhenry.com/role/OtherAssetsOtherIntangibleAssetsDetails">
        <link:definition>9954498 - Disclosure - Other Assets Other Intangible Assets (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="OtherAssetsFutureAmortizationExpenseDetails" roleURI="http://www.jackhenry.com/role/OtherAssetsFutureAmortizationExpenseDetails">
        <link:definition>9954499 - Disclosure - Other Assets Future Amortization Expense (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DebtNarrativeDetails" roleURI="http://www.jackhenry.com/role/DebtNarrativeDetails">
        <link:definition>9954500 - Disclosure - Debt Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ProvisionForIncomeTaxesDetails" roleURI="http://www.jackhenry.com/role/ProvisionForIncomeTaxesDetails">
        <link:definition>9954501 - Disclosure - Provision For Income Taxes (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="DeferredTaxLiabilityDetails" roleURI="http://www.jackhenry.com/role/DeferredTaxLiabilityDetails">
        <link:definition>9954502 - Disclosure - Deferred Tax Liability (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EffectiveTaxRateReconciliationDetails" roleURI="http://www.jackhenry.com/role/EffectiveTaxRateReconciliationDetails">
        <link:definition>9954503 - Disclosure - Effective Tax Rate Reconciliation (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IncomeTaxesNarrativeDetails" roleURI="http://www.jackhenry.com/role/IncomeTaxesNarrativeDetails">
        <link:definition>9954504 - Disclosure - Income Taxes Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="UnrecognizedTaxBenefitsDetails" roleURI="http://www.jackhenry.com/role/UnrecognizedTaxBenefitsDetails">
        <link:definition>9954505 - Disclosure - Unrecognized Tax Benefits (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="IndustryandSupplierConcentrationsConcentrationRiskDetails" roleURI="http://www.jackhenry.com/role/IndustryandSupplierConcentrationsConcentrationRiskDetails">
        <link:definition>9954506 - Disclosure - Industry and Supplier Concentrations Concentration Risk (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="StockBasedCompensationNarrativeDetails" roleURI="http://www.jackhenry.com/role/StockBasedCompensationNarrativeDetails">
        <link:definition>9954507 - Disclosure - Stock Based Compensation Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="UnitAwardsDetails" roleURI="http://www.jackhenry.com/role/UnitAwardsDetails">
        <link:definition>9954508 - Disclosure - Unit Awards (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="UnitAwardMeasurementDateAssumptionsDetails" roleURI="http://www.jackhenry.com/role/UnitAwardMeasurementDateAssumptionsDetails">
        <link:definition>9954509 - Disclosure - Unit Award Measurement Date Assumptions (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EarningsPerShareDetails" roleURI="http://www.jackhenry.com/role/EarningsPerShareDetails">
        <link:definition>9954510 - Disclosure - Earnings Per Share (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EmployeeBenefitsPlansEmployeeStockPurchasePlanDetails" roleURI="http://www.jackhenry.com/role/EmployeeBenefitsPlansEmployeeStockPurchasePlanDetails">
        <link:definition>9954511 - Disclosure - Employee Benefits Plans Employee Stock Purchase Plan (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="EmployeeBenefitsPlans401kDetails" roleURI="http://www.jackhenry.com/role/EmployeeBenefitsPlans401kDetails">
        <link:definition>9954512 - Disclosure - Employee Benefits Plans 401(k) (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="BusinessAcquisitionsDetails" roleURI="http://www.jackhenry.com/role/BusinessAcquisitionsDetails">
        <link:definition>9954513 - Disclosure - Business Acquisitions (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ReportableSegmentInformationNarrativeDetails" roleURI="http://www.jackhenry.com/role/ReportableSegmentInformationNarrativeDetails">
        <link:definition>9954514 - Disclosure - Reportable Segment Information Narrative (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="ReportableSegmentInformationReconciliationofOperatingProfitbySegmenttoConsolidatedDetails" roleURI="http://www.jackhenry.com/role/ReportableSegmentInformationReconciliationofOperatingProfitbySegmenttoConsolidatedDetails">
        <link:definition>9954515 - Disclosure - Reportable Segment Information Reconciliation of Operating Profit by Segment to Consolidated (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
      <link:roleType id="SubsequentEventsDetails" roleURI="http://www.jackhenry.com/role/SubsequentEventsDetails">
        <link:definition>9954516 - Disclosure - Subsequent Events (Details)</link:definition>
        <link:usedOn>link:presentationLink</link:usedOn>
        <link:usedOn>link:calculationLink</link:usedOn>
        <link:usedOn>link:definitionLink</link:usedOn>
      </link:roleType>
    </xs:appinfo>
  </xs:annotation>
  <xs:element id="jkhy_NatureOfOperationsAndSummaryOfSignificantAccountingPoliciesAbstract" abstract="true" name="NatureOfOperationsAndSummaryOfSignificantAccountingPoliciesAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="jkhy_ScheduleOfShareBasedPaymentAwardRSUValuationAssumptionsTableTextBlockTableTextBlock" abstract="false" name="ScheduleOfShareBasedPaymentAwardRSUValuationAssumptionsTableTextBlockTableTextBlock" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:textBlockItemType"/>
  <xs:element id="jkhy_EntityNumberOfCustomers" abstract="false" name="EntityNumberOfCustomers" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="xbrli:integerItemType"/>
  <xs:element id="jkhy_PurchaseofInvestmentAbstract" abstract="true" name="PurchaseofInvestmentAbstract" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:stringItemType"/>
  <xs:element id="jkhy_AutomatedBookkeepingInc.Member" abstract="true" name="AutomatedBookkeepingInc.Member" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_OutsourcingCloudMember" abstract="true" name="OutsourcingCloudMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ProductDeliveryandServiceMember" abstract="true" name="ProductDeliveryandServiceMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_InHouseSupportMember" abstract="true" name="InHouseSupportMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ProcessingMember" abstract="true" name="ProcessingMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ElizabethtownKYSubleaseMember" abstract="true" name="ElizabethtownKYSubleaseMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_AccumulatedAmortizationOperatingLeaseRightofuseasset" abstract="false" name="AccumulatedAmortizationOperatingLeaseRightofuseasset" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_OperatingLeaseLiabilityOptionToExtendAmounts" abstract="false" name="OperatingLeaseLiabilityOptionToExtendAmounts" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_LesseeLeaseNotYetCommencedFutureMinimumPaymentsDue" abstract="false" name="LesseeLeaseNotYetCommencedFutureMinimumPaymentsDue" nillable="true" xbrli:periodType="instant" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_CoreSegmentMember" abstract="true" name="CoreSegmentMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_PaymentsMember" abstract="true" name="PaymentsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ComplementaryMember" abstract="true" name="ComplementaryMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ComputerSoftwaretobeSoldLeasedorMarketedMember" abstract="true" name="ComputerSoftwaretobeSoldLeasedorMarketedMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_InternalUseComputerSoftwareMember" abstract="true" name="InternalUseComputerSoftwareMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_DeferredTaxAssetsLeasingLiability" abstract="false" name="DeferredTaxAssetsLeasingLiability" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_FairvalueongrantdatelessPVofdividendsMember" abstract="true" name="FairvalueongrantdatelessPVofdividendsMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_FairvalueunderMonteCarloMember" abstract="true" name="FairvalueunderMonteCarloMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_A2015EIPMember" abstract="true" name="A2015EIPMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_ShareBasedPaymentArrangementExpenseNetTaxShortfall" abstract="false" name="ShareBasedPaymentArrangementExpenseNetTaxShortfall" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ShareBasedPaymentArrangementExpenseNetExcessTaxBenefit" abstract="false" name="ShareBasedPaymentArrangementExpenseNetExcessTaxBenefit" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationPeriodAfterTerminationOfEmployment" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationPeriodAfterTerminationOfEmployment" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationPeriodAfterDeath" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationPeriodAfterDeath" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationAfterGrantDate" abstract="false" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardTerminationAfterGrantDate" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_OtherValuationApproachMember" abstract="true" name="OtherValuationApproachMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_CompensationPeerGroupMember" abstract="true" name="CompensationPeerGroupMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_BeginningPercentileRankForTotalShareReturnTSR" abstract="false" name="BeginningPercentileRankForTotalShareReturnTSR" nillable="true" xbrli:periodType="instant" substitutionGroup="xbrli:item" type="dtr-types1:percentItemType"/>
  <xs:element id="jkhy_EmployeeStockPurchasePlanMember" abstract="true" name="EmployeeStockPurchasePlanMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:domainItemType"/>
  <xs:element id="jkhy_Employeestockpurchaseplanaveragepricepershare" abstract="false" name="Employeestockpurchaseplanaveragepricepershare" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types1:perShareItemType"/>
  <xs:element id="jkhy_DefinedContributionPlanAgeRequirement" abstract="false" name="DefinedContributionPlanAgeRequirement" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:pureItemType"/>
  <xs:element id="jkhy_DefinedContributionPlanEmploymentLengthRequirement" abstract="false" name="DefinedContributionPlanEmploymentLengthRequirement" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="xbrli:durationItemType"/>
  <xs:element id="jkhy_PayrailzMember" abstract="true" name="PayrailzMember" nillable="true" xbrli:periodType="duration" substitutionGroup="xbrli:item" type="dtr-types:domainItemType"/>
  <xs:element id="jkhy_EscrowDepositRelatedToAcquisitionTotal" abstract="false" name="EscrowDepositRelatedToAcquisitionTotal" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_EscrowDepositFinalPurchasePriceAdjustment" abstract="false" name="EscrowDepositFinalPurchasePriceAdjustment" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_EscrowDepositIndemnificationMatters" abstract="false" name="EscrowDepositIndemnificationMatters" nillable="true" xbrli:periodType="instant" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfRevenueFromCoreToCorporateAndOther" abstract="false" name="ReclassificationOfRevenueFromCoreToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfRevenueFromPaymentsToCorporateAndOther" abstract="false" name="ReclassificationOfRevenueFromPaymentsToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="credit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfRevenueFromComplementaryToCorporateAndOther" abstract="false" name="ReclassificationOfRevenueFromComplementaryToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfCostFromCoreToCorporateAndOther" abstract="false" name="ReclassificationOfCostFromCoreToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfCostFromPaymentsToCorporateAndOther" abstract="false" name="ReclassificationOfCostFromPaymentsToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
  <xs:element id="jkhy_ReclassificationOfCostFromComplementaryToCorporateAndOther" abstract="false" name="ReclassificationOfCostFromComplementaryToCorporateAndOther" nillable="true" xbrli:periodType="duration" xbrli:balance="debit" substitutionGroup="xbrli:item" type="xbrli:monetaryItemType"/>
</xs:schema>
