Stoney Creek was first inhabited by Canadian First Nations and later explored by French-Canadian fur traders before the area was first settled by Loyalists fleeing the American Revolution in the late 1700s. The name 'Stoney Creek' is borrowed from the area's central water feature, 'the Stoney Creek' which runs from the Devil's Punchbowl, in the Niagara Escarpment, to Lake Ontario. It is often taken for granted that the 'Stoney Creek' is a description of the creek's rockiness although there is some historical evidence to suggest that the name comes from an early settler in the area whose family name was 'Stoney'.

On 6 June 1813 the settlement garnered some notability during the War of 1812 as the site of the eponymous battle. After being informed of American troop movements by Billy Green, a local hero and the namesake of Billy Green elementary school, British forces overwhelmed the Americans in a surprise night attack.