In 1903, Hamilton Hill Primary School was opened to ease the pressure of numbers on Coogee Primary School. The original classrooms built in 1903 remain on the site and have been heritage listed by the Cockburn Council. When the old Hamilton Hill School closed, the site was occupied in 1989 by Southern Christian Academy, which changed its name to Calvary Christian College in 1993.
In 2003 the College was adopted by New Life Christian Community, a vibrant and growing church in Fremantle, and re-named New Life Christian College.
Early in 2014 the Board, in keeping with their belief that the College would eventually have a significant regional impact, re-branded the school and changed its name to Fremantle Christian College. An application to extend the year levels of the College was submitted shortly after and approval was granted by the Minister for Education in August 2014.