In 1864, three parishioners of St Paul's Anglican Church at Rondebosch met with the incumbent priest, John Harries Thomas to discuss the raising of another mission school.  Permission was readily given and Sophy Gray, wife of the first Bishop of Cape Town, was commissioned to draw the plans.  The small stone structure with thatch roof that resulted was called the Camp Ground Road Mission School Chapel and was opened in July 1865.

From its earliest days, St Paul's provided Sunday religious instruction at the school; as time went by church services became progressively more important and, by the end of the nineteenth century, were its only function.  The fact that St Thomas's had become a church and not a school, raised administrative complications and it took the passage through parliament of the Rondebosch Church Lands Act of 1909 for the Diocesan Trustees to obtain full title to St Thomas's Church and its precincts.  St Thomas's continued as a satellite of St Paul's until April 1947 when it became an independent parish with its own rector and church council.

In 1964 it was decided to establish a Centenary fund so that the centenary cuold be marked by an enlargement to the church.  North and South transepts were added to boost the capacity to +/- 400 and the thatched roof was replaced with dark red tiles.  Vestries and cloakrooms were added and the entrance porch enlarged with the door facing away from the noise of passing traffic.  This work was completed in 1967.