The oldest human artifacts found in Whitchurch Township date back to 1500 BC and were found in the hamlet of Ringwood (now part of urban Stouffville). Prior to the arrival of Europeans, two Native trails pass over through what is today Whitchurch–Stouffville. The Vandorf Trail and the Rouge Trail both were part of the aboriginal and Coureur des bois trail system running through dense forests from Lake Ontario to Lake Simcoe.

In 2003, a large 16th-century Huron village was observed in Stouffville. In 2012, archaeologists admitted that a European forged-iron axehead was discovered at the site--"the earliest European piece of iron ever found in the North American interior."

Whitchurch was one of 19 counties established in 1792, by John Graves Simcoe, the first Lieutenant-Governor of Upper Canada. Whitchurch is named after a town in Herefordshire, England, which was the birthplace of Simcoe’s wife Elizabeth. By the 1840s Whitchurch had 59 grist mills and 186 saw mills running from the base of the many creeks and rivers that flowed through this county.
The Village of Stouffville was established in 1804, by Abraham and Elizabeth Stouffer.. The Stouffer family founded their own saw and grist mills at the intersection of what is now Main and Mill Streets. Soon a whole village including a school, church and general store were added to this community.

The Toronto & Nipissing Railway appeared in Stouffville in 1871. The same year Stouffville was incorporated as a Village. Stouffville saved its Village status for 100 years until 1971, when it amalgamated with Whitchurch Township to form what is now the Town of Whitchurch-Stouffville.