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

<!--XBRL Document Created with Wdesk from Workiva-->
<!--Copyright 2021 Workiva-->
<!--r:552a984a-1215-49b3-b4c6-7164ad3d9112,g:a9100c03-66bc-476a-a37e-7a21e52b1f5f-->
<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" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <link:roleRef roleURI="http://www.exagen.com/role/Cover" xlink:type="simple" xlink:href="exdx-20201231.xsd#Cover"/>
  <link:calculationLink xlink:role="http://www.exagen.com/role/Cover" xlink:type="extended"/>
</link:linkbase>
