One of a chain of three forts in Wisconsin built by the U.S. Army along the Fox-Wisconsin waterway (Fort Howard at Green Bay 1816, Fort Crawford at Prairie du Chien 1816, Fort Winnebago at Portage). The Army arrived in September 1828 from Green Bay, took possession of the land and began building a permanent fort in 1829.

Among the officers supervising the construction was a young lieutenant, Jefferson Davis. The fort was maintained at the portage until 1845 when the last garrison was transferred out. The buildings and property were ordered sold in December 1853. Deeds transferring the property were signed by Jefferson Davis, who was now the Secretary of War in Washington, DC.