The history of Manitoba covers the period from the arrival of Paleo-Indians thousands of years ago to the present day. When European fur traders first travelled to the area present-day Manitoba, they developed trade networks with several First Nations. European fur traders in the area during the late-17th century, with the French under Pierre Gaultier de Varennes, sieur de La Vérendrye set up several trading post forts. In 1670, Britain declared sovereignty over the watershed of Hudson's Bay, known as Rupert's Land; with the Hudson's Bay Company granted a commercial monopoly over the territory.

At the end of the French and Indian War in 1763, the French colony of New France was ceded to the British, ending any competition between European claims to the North-West. Traders from the Hudson's Bay Company expanded their operations to areas formerly occupied by French fur trading forts. In 1811, Lord Selkirk established the first agricultural settler colony in Rupert's Land, the Red River Colony, around the Red River of the North. In 1817 Saulteaux Chief Peguis and four other Chiefs of the Sauteaux and Cree Nations agreed to share land with Lord Selkirk and his settlers in the Peguis Selkirk Treaty. As a result of the Treaty of 1818 between the United Kingdom and the United States the 49th parallel north was established as the border between Rupert's Land and the United States; with areas south of the parallel being transferred to the United States.

In 1870, the Deed of Surrender was enacted, transferring Rupert's Land from the United Kingdom to Government of Canada, forming the North-West Territories. In response to the Red River Rebellion, the province of Manitoba was established around the lands of the Red River Colony. Canada started a process of Numbered Treaties with the First Nations to settle aboriginal title in the North-West and clear land for settlers. Manitoba is the first province created from the North-West Territories, and was subsequently expanded in 1881 and 1912 to its present boundaries. The economy was long based on farming, grains, cattle, and hay. The economy is now diversified due to urbanization.

The geographical area of modern-day Manitoba was inhabited by the First Nations people shortly after the last ice age glaciers retreated in the south-west approximately 10,000 years ago; the first exposed land was the Turtle Mountain area. The first humans in southern Manitoba left behind pottery shards, spear and arrow heads, copper, petroforms, pictographs, fish and animal bones, and signs of agriculture along the Red River near Lockport, Manitoba, where corn and other seed crops were planted.

Eventually there were aboriginal settlements of Ojibwa, Cree, Dene, Sioux, Mandan, and Assiniboine peoples, along with other tribes that entered the area to trade. There were many land trails made as a part of a larger native trading network on both land and water. The Whiteshell Provincial Park region along the Winnipeg River has many old petroforms and may have been a trading centre, or even a place of learning and sharing of knowledge for over 2000 years. The cowry shells and copper are proof of what was traded as a part of a large trading network to the oceans, and to the larger southern native civilizations along the Mississippi and in the south and south-west.

In Northern Manitoba there are areas that were mined for quartz to make arrow heads. For thousands of years there have been humans living in this region, and there are many clues about their ways of life.

Henry Hudson, in 1611, was one of the first Europeans to sail into what is now known as Hudson Bay. The first European to reach what is now northern Manitoba was Sir Thomas Button in 1612, who named the Nelson River. Button was a member of the "Company of the Merchants Discoverers of the North-West Passage" and he hoped to find a trade route to China. Henry Kelsey was the first European to travel from Hudson Bay to the prairies, reporting the buffalo and grizzly bears that he saw. Kelsey went as far as present day Saskatchewan. The Hudson's Bay Company traded with native fur traders that canoed far and wide along the many rivers of present-day Manitoba. Rupert's Land was the first name given to the area by Europeans, encompassing the Hudson Bay watershed. Pierre Gaultier de Varennes, sieur de La Vérendrye, visited the Red River Valley in the 1730s as part of opening the area for French exploration and exploitation. As French explorers entered the area, a Montreal-based company, the North West Company, began trading with the Métis.

When the British ship Nonsuch sailed into Hudson Bay in 1668–1669, she was the first fur trading vessel to reach the area; that voyage led to the formation of the Hudson's Bay Company, to which the British government gave absolute control of the entire Hudson Bay watershed. This watershed was named Rupert's Land, after Prince Rupert, who helped to subsidize the Hudson's Bay Company. York Factory was founded in 1684 after the original fort of the Hudson's Bay Company, Fort Nelson (built in 1682), was destroyed by rival French traders. Shortly after the Battle of Hudson's Bay, York Factory was briefly occupied by French forces. Fur trading forts were built by both the North West Company and the Hudson's Bay Company along the many rivers and lakes, and there was often fierce competition with each other in more southern areas.