Although not within the military stockade, the Surgeons' Quarters is the only remaining building of Fort Winnebago. The other buildings and stockade were destroyed by fire caused by tenants after the Army had left the area.

Built between 1819-1824, the Surgeons' Quarters is a true example of the log houses built by French settlers in early Wisconsin. It was built by Francois LeRoi, who had controlled the portaging operations between the two rivers. With increased competition from the American Fur Company and others at the portage, LeRoi sold the log house to the U.S. Army in 1828, who used it as a sutler's store for six years, then modified it to be used by the fort's medical officer. A hospital was built nearby that same year.

Surgeon Lyman Foote, who arrived in 1834, was probably the first doctor to occupy the Surgeons' Quarters; his predecessors had been housed in the Officers' Quarters in the fort itself. Surgeon Foote served at Fort Winnebago for five years. His successor, Surgeon C. H. Laub, remained until the last garrison left in 1845.