Various clues point to Winnebago intrusion into Wisconsin from the Southeast. At the time of contact, most of the people congregated in a large village, Red Banks, on the south side of Green Bay. The French learned of the Winnebago from the Ottawa in the early 1620s, though it was not until 1665 that documentation of Winnebago history began. At that time they had recently experienced a period of intertribal wars, epidemics, and famine and were reduced to some 450 to 600 people in all. They made peace and intermarried with neighboring tribes, eventually recouping their population loss. Borrowing extensively from other Algonkian-speaking tribes, they reorganized their socioeconomic patterns to engage in the fur trade. By the eighteenth century, the tribe had withdrawn from Green Bay, and the village groups began separating. They eventually gained firm control of an area bounded on the east and south by Lake Winnebago and the Rock River, on the north and east by the Fox-Wisconsin portage route and the Black River, and on the west by the eastern watershed of the Mississippi River, their territory extending to the river north of Prairie du Chien. They occupied more than thirty villages of one hundred to three hundred people each, trading at major fur company posts in Portage and Prairie du Chien and with independent traders.
The Winnebago signed boundary treaties with the United States in 1825, 1827, and 1828, and treaties ceding their southern lands between the Rock and lower Wisconsin rivers in 1829 and 1832. The Winnebagos' remaining Wisconsin land between the Mississippi and upper Wisconsin rivers was not adequate to support all the people and the 1832 treaty provided a reservation along the Mississippi in Iowa. When the government wanted their last Wisconsin land, the Winnebago sent a delegation to Washington to oppose the sale. Pressured to sign a treaty if they hoped to return home, the group agreed to a treaty that gave them only eight months to move, which created a permanent split in the tribe. The southern villagers, whose land had been overrun by lead miners and already ceded had little recourse but to accept removal, but the northern villagers repudiated the treaty and led a fugitive existence in Wisconsin for nearly three decades. The removed group signed treaties in 1846 and 1855 for new reservations, ending up at Blue Earth, Minnesota. The 1862 Sioux uprising in Minnesota prompted an executive order to remove them along with the dissident Sioux. By the summer of 1863, all had fled the barren land assigned to them in South Dakota, with about twelve hundred arriving among the Omaha in Nebraska. In 1865, they ceded their South Dakota land by treaty for a reservation on what had been the northern strip of the Omaha reservation.
The government initiated allotment in 1871 which was completed under the General Indian Allotment Act of 1887. Generally, the people settled in the unallotted timber land along the Missouri River. They leased and later sold their farmland to Whites. By World War I, most of the western two-thirds of the reservation had passed out of Winnebago ownership. The Indian Bureau repressed traditional leadership and social organization. When the Indian Reorganization Act was passed in 1934, the Nebraska Winnebago established a constitutional government under its provisions.
After 1837, the defiant Winnebago hiding out in central Wisconsin were periodically rounded up by the government and moved to whatever reservation the rest of the tribe currently occupied. But they always returned to Wisconsin. When the Homestead Act of 1862 was extended to Indians, some Wisconsin Winnebago took up homesteads after 1874, but many were afraid to appear before White authorities. In 1881, all the Wisconsin Winnebago were assigned homesteads under special legislation. They retained many of their governing and religious structures. Settlements sprang up with a western focus in the Black River Falls area, where the Evangelical and Reform church established a mission and day school in 1878 and later a boarding school at Neillsville, and an eastern focus near Wittenberg, where a Norwegian Lutheran mission and boarding school opened at Tomah in the 1890s. As the twentieth century wore on, traditional religion and with it traditional social organization came under increasing threat from inroads of mission Christianity and the Peyote or Native American Church.
A new sense of tribal unity was set in motion in Wisconsin when the people elected a claims committee in 1947 to work with the Nebraska tribal council on a common claim before the U.S. Indian Claims Commission. The claim of about $4.5 million was not settled until the late 1970s, when both the Nebraska and Wisconsin groups opted for per-capita payments that were soon spent. The Wisconsin group's economic condition had steadily worsened after World War II and led to organization under the Indian Reorganization Act in 1962. They acquired land under tribal trust status at their major settlements to qualify for housing and other federal benefits. Political power struggles occurred over programmed federal funding, but the late 1980s brought increasing stability under new federal policies of self-determination and the generation of unencumbered income from bingo and smoke shops.