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The first white settlement on the shores of Thunder Bay was in 1683/1684, a French trading post put up by Daniel Greysolon, Sieur du Lhut. It was shut down by the French authorities in 1696.

In 1717, Zacharie Robutel de la Noue established Fort Caministogoyan near the ruins of the previous fort, but that was abandoned about 1760 due to the British conquest. The British preferred to trade in Grand Portage in what is now Minnesota.

The Jay Treaty of 1794 forced them out of Minnesota, and by 1803 the British were back at Fort Kaministiquia. It was the main fur trading post for the NWC until 1821 when it merged with HBC, and the operations shifted to York Factory. It was renamed Fort William, after its founder William MacGillivray, in 1807. The site fell into disrepair and never really recovered, but did operate as a minor post throughout the 19th century. So 1803 is generally regarded as the beginning of permanent settlement here.

In 1858, with the signing of the Superior-Robertson Treaty, the new Canadian government surveyed an area near Fort William called "Town Plot" with the intention of establishing an urban community. This was the first non-fur-trading community establishment in the area. From this point forward, there is an actual village in the Fort William area. So 1858 is the earliest date for the actual town's existence. Few records exist from this era, but artifacts spanning the 1850s to 1870s exist throughout the Town Plot and Fort William areas, so there was some form of actual habitation there. The oldest house still standing in the city dates to 1877 and was associated an unorganized settlement near "the river", and was moved several miles to its present location in 1907 by which time the fort was pretty much defunct.

In 1873, the Municipality of Shuniah was formed as the first local government. In 1881, the townships around Fort William separated and became the Municipality of Neebing. The railway arrived in 1883, and slowly took over the site of Fort William (the fort) to construct railway facilities. The last remaining pieces of the old fort were destroyed sometime in the 1950s, but stone foundations and log pilings still exist under the rail yard to this day.

Prince Arthur's Landing, a Canadian military outpost that grew into a village, separated from Shuniah in 1884, and Fort William separated from Neebing in 1892. Fort William and Port Arthur both became cities in 1907 (Fort William wasn't actually large enough but the government had to treat both cities equal) and amalgamated into Thunder Bay in 1970. Port Arthur was the county seat for Thunder Bay District since it is where the military and law courts were located at the time. Fort William's courthouse until the 1970s was just a room in the police station.