The present Gothic Revival church building dates from 1843 and was designed by architect John George Howard.

Services for what became the congregation of St. John's, York Mills, began in the Bedford Park home of Seneca Ketchum (1772–1850).

Dr. John Strachan, Rector of St. James Church and later 1st Bishop of Toronto, occasionally conducted services for Ketchum's group.

[4] Joseph Shepard donated a parcel of land fronting Yonge Street for the construction of the church.

The church employed Upper Canada's leading architect of the time, John George Howard.

[12] The first burial in the churchyard was in 1806 of the seven-year-old grandson of Cornelius van Nostrand who had come to York Mills as a Loyalist in 1797.

[12] Many of the early settlers of the area and participants in the Upper Canada Rebellion are buried in the church cemetery.

Archbishop Derwyn Owen, Primate of All Canada,[14] Lionel Conacher,[15] Walter Seymour Allward and a memorial to the van Nostrand family.