I 1970, da hans mor fortalte ham at han skulle trække nummer til militæret, meldte han sig til [[United States Marine Corps|U.S. Marine Corps]].<ref name=nomination/><ref name=brighton/><ref name=10things/> Han tjente i en [[infanteri]]-deling med [[2nd Marine Division (USA)|2nd Marine Division]] i [[Camp Lejeune]], [[North Carolina]], og kom i den inaktive reserve som [[sergent]] i 1972, så han kunne komme på [[college]].<ref name=nomination/><ref name=brighton/><ref name=10things/> Han vendte tilbage til aktiv tjeneste i marinekorpeset i 1975, og færdiggjorde en uddannelse på [[Officer Candidates School (United States Marine Corps)|Officer Candidates School]], og fik titel af 2. løjtnant den 27. december 1975.<ref name=nomination/><ref name=OfficialBio>{{cite web | title=John F. Kelly, Former Commander, U.S. Southern Command | url=http://www.defense.gov/About-DoD/Biographies/Biography-View/Article/602724/john-f-kelly | publisher=[[U.S. Department of Defense]] | access-date=13. december 2016 | archive-date=10. december 2016 | df=mdy-all | archive-url=https://web.archive.org/web/20161210193221/http://www.defense.gov/About-DoD/Biographies/Biography-View/Article/602724/john-f-kelly | url-status=live }}</ref> I 1976 blev han færdig på [[University of Massachusetts Boston]] og i 1984 fik han en [[kandidatgrad]] i [[sikkerhedspolitik]] fra [[Georgetown School of Foreign Service]].<ref name=nomination/><ref>{{cite web | title=Secretary Johnson Swears in New Members of the Homeland Security Advisory Council | url=https://www.dhs.gov/news/2016/06/02/secretary-johnson-swears-new-members-homeland-security-advisory-council | publisher=[[U.S. Department of Homeland Security]] | date=2. juni 2016 | archive-date= 2. februar 2017 | df=mdy-all | access-date= 1. maj 2018 | archive-url=https://web.archive.org/web/20170202053716/https://www.dhs.gov/news/2016/06/02/secretary-johnson-swears-new-members-homeland-security-advisory-council | url-status=live }}</ref> I 1995 færdiggjorde Kelly en uddannelse fra [[National Defense University]] i Washington, DC med en kandidatgrad i Science in Strategic Studies.
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