The Presbyterian Theological College began in 1866 as the Theological Hall of the Presbyterian Church of Victoria. From 1868 the College was run from Chalmers Church in the suburb of Eastern Hill. In 1871, it was moved to the Old Assembly Hall in Collins Street, Melbourne, then 10 years later to Ormond College, University of Melbourne.

In 1974, the whole staff of the Theological Hall opted to join with the Uniting Church. The continuing Presbyterian Church of Victoria opened a provisional college in Hawthorn, with a small number of staff and students. The college relocated to the top floor of the Assembly Hall building in Melbourne in 1977, and following growth in enrolments, purchased its current Box Hill North campus in 1986.

The Box Hill North campus was renovated and extended in 1990, with the full building programme completed in 1996 with the expansion of the Swanton Library. A block of six residential units for students were opened on the college property in 2008.