Elder William Clarke, Sr., was one of the group who withdrew from the "Auld Kirk" at the Synod Meeting held in Kingston, Canada West in July, 1844; his Minister, Rev.

The original Knox Congregation (named after Scottish Church reformer John Knox) met first with another congregation located in York Mills, until settling in the developing Scarborough Township village of Agincourt.

In 1853, it became the centre of the "Scarborough Township Pastoral Charge", along with Melville (formed 1851) in West Hill, Zion Church, Cedar Grove (formed 1855), in Markham Township, Chalmers Church, York Town Line (1863–1890), and other occasional preaching points.

This church still stands at the corner of Sheppard Avenue East and Midland Avenue, surrounded by a large cemetery containing many early settlers, and a number of prominent Church leaders.

A number of members left to form a "Continuing" Knox Presbyterian Church, now located nearby at 4156 Sheppard Avenue East.