The university descends from two Anglican teacher training colleges, which were founded in York in 1841 (for men) and 1846 (for women). York St John University's founding mission was to improve access to education for people from all walks of life.[5] In 1862, the women's college relocated to Ripon. Over the next century, the colleges gradually diversified their education programmes. The colleges, St John's College (named for John the Evangelist)[6][7] and Ripon College, merged in 1974 to form the "College of Ripon and York St John".

In 1990 the combined institution formally became a college of the University of Leeds; this arrangement allowed it to award degrees in the name of the latter, while remaining in practice largely autonomous. Between 1999 and 2001, all activities were transferred to York and the college received the name "York St John College".

In February 2006, the College was granted the right to award degrees in its own name and the right to call itself a university college. On 10 July 2006 the Privy Council approved a request from the college to become a full-fledged university; the name became "York St John University" on 1 October 2006, and the first Chancellor (installed at a ceremony in York Minster on 7 March 2007) was the Archbishop of York John Sentamu. Archbishop Sentamu retired in 2019 after 12 years as Chancellor. He was succeeded by BBC broadcaster Reeta Chakrabarti.