In 1820, the first Presbyterian congregation in Toronto (then the Town of York) was formed, and after the donation of land from Jesse Ketchum, built a church on Richmond Street.

This church was known as First Presbyterian Congregation of York, Upper Canada, and James Harris (later to be Ketchum's son in law) became minister.

This dispute hit the Canadas the following year at the respective Synod Meetings in Kingston and Nova Scotia; a faction broke off from St. Andrew's, who remained in the "Auld" Kirk.

The congregation built a new larger church on the same lot, this time facing Queen Street West between Yonge and Bay.

Knox quickly became the leading Free Church congregation in Canada, helping to spread the movement throughout the colony.

At the time Toronto had strict Lord's Day laws that prevented public transit from running on Sundays, making it imperative that churches be located near to the population.

Dr. William Fitch, who arrived in early 1955 from the Springburn area of Glasgow, Scotland, the congregation built an adjoining hall (Knox Fellowship Centre) in 1961, and expanded its ministries into the inner city (Evangel Hall at 573 Queen Street West had been run by Knox since 1913), the Universities (including Ryerson and York, and community colleges such as nearby George Brown College), and during the summer months, began the weekly Knox Summer Fellowship, Wednesday Evening Services that brought (or introduced) renowned speakers from around the world.