In 1793, Lieutenant Governor John Graves Simcoe authorized a garrison on the present site of Fort York, just west of the mouth of Garrison Creek on the north western shore of Lake Ontario. Simcoe recognized Toronto was an ideal site for settlement and defence because of its natural harbour and relative longer distance from the United States. Fort York guards the western (at the time of construction, the only) entrance to the bay. Simcoe had decided to make Toronto (which he renamed York) the capital of Upper Canada, and the government, the first parliament buildings and the town were established one and a half miles east of the fort (near the foot of the present Parliament Street).

During the War of 1812, in the Battle of York, on 27 April 1813, U.S. army and naval forces attacked York from Lake Ontario, overrunning the garrison. As the British abandoned the fort, they set the powder magazine to blow up, killing or wounding several hundred U.S. soldiers (including General Zebulon Pike, for whom Pikes Peak is named). The U.S. destroyed what was left of the garrison and burned much of the settlement of York, including the Parliament Buildings during their five-day occupation. They had defeated outnumbered British, Canadian, and First Nations forces, but with the loss of many more men. Following several more U.S. raids over the summer, the British garrison returned to York and rebuilt the fortifications, most of which are still standing today. The rebuilt fort was sufficient to repel a further attempted invasion in 1814.

The British Army had occupied Fort York from 1793 but transferred the site to the Government of Canada in 1869, shortly after Canadian Confederation. The Department of Militia and Defence continued to use the site as a military establishment until 1880, and again during the First and Second World Wars. 

The site was threatened in 1905 by a proposed streetcar route to the CNE, which would have divided the fort property in two. Following an outcry, the line was not built through the fort. Later in 1909, the Department of Militia and Defence later transferred the property to the City of Toronto with the provision that the city would preserve the Fort’s historic structures. On 25 May 1923, the Fort was established as a National Historic Site of Canada. The city undertook restoration work and the Fort was opened to the public in 1934.