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

<!--XBRL Document Created with the Workiva Platform-->
<!--Copyright 2025 Workiva-->
<!--r:9e9182f1-0f3a-4ae0-bdd2-b7ee3974d95a,g:b8706b75-9d59-4938-aa17-09b35094523b-->
<link:linkbase xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/all" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" xlink:type="simple" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member"/>
  <link:roleRef roleURI="http://xbrl.sec.gov/ecd/role/PvpAdjustmentsOnly" xlink:type="simple" xlink:href="https://xbrl.sec.gov/ecd/2025/ecd-2025.xsd#PvpAdjustmentsOnly"/>
  <link:definitionLink xlink:role="http://xbrl.sec.gov/ecd/role/PvpAdjustmentsOnly" xlink:type="extended">
    <link:loc xlink:type="locator" xlink:label="loc_ecd_AllAdjToCompMember" xlink:href="https://xbrl.sec.gov/ecd/2025/ecd-2025.xsd#ecd_AllAdjToCompMember"/>
    <link:loc xlink:type="locator" xlink:label="loc_jkhy_EquityAwardsReportedValueMember_7ed1672f-3f81-4ae7-abe2-2a64d6d30a94" xlink:href="jkhy-20251001.xsd#jkhy_EquityAwardsReportedValueMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember" xlink:to="loc_jkhy_EquityAwardsReportedValueMember_7ed1672f-3f81-4ae7-abe2-2a64d6d30a94" xlink:type="arc" order="4"/>
    <link:loc xlink:type="locator" xlink:label="loc_jkhy_EquityAwardsGrantedDuringTheYearUnvestedMember_f567e974-48f1-4963-9372-357697161a04" xlink:href="jkhy-20251001.xsd#jkhy_EquityAwardsGrantedDuringTheYearUnvestedMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember" xlink:to="loc_jkhy_EquityAwardsGrantedDuringTheYearUnvestedMember_f567e974-48f1-4963-9372-357697161a04" xlink:type="arc" order="5"/>
    <link:loc xlink:type="locator" xlink:label="loc_jkhy_EquityAwardsGrantedInPriorYearsUnvestedMember_713f52ee-7a26-4baa-aefb-ceae8aa99487" xlink:href="jkhy-20251001.xsd#jkhy_EquityAwardsGrantedInPriorYearsUnvestedMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember" xlink:to="loc_jkhy_EquityAwardsGrantedInPriorYearsUnvestedMember_713f52ee-7a26-4baa-aefb-ceae8aa99487" xlink:type="arc" order="6"/>
    <link:loc xlink:type="locator" xlink:label="loc_jkhy_EquityAwardsGrantedInPriorYearsVestedMember_0416baeb-e405-4260-94ff-516ed19e7263" xlink:href="jkhy-20251001.xsd#jkhy_EquityAwardsGrantedInPriorYearsVestedMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember" xlink:to="loc_jkhy_EquityAwardsGrantedInPriorYearsVestedMember_0416baeb-e405-4260-94ff-516ed19e7263" xlink:type="arc" order="7"/>
    <link:loc xlink:type="locator" xlink:label="loc_jkhy_EquityAwardsThatFailedToMeetVestingConditionsMember_2f14809a-3dd0-4d9a-99eb-33bb4c184736" xlink:href="jkhy-20251001.xsd#jkhy_EquityAwardsThatFailedToMeetVestingConditionsMember"/>
    <link:definitionArc xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="loc_ecd_AllAdjToCompMember" xlink:to="loc_jkhy_EquityAwardsThatFailedToMeetVestingConditionsMember_2f14809a-3dd0-4d9a-99eb-33bb4c184736" xlink:type="arc" order="8"/>
  </link:definitionLink>
</link:linkbase>
