Fort Atkinson was named after General Henry Atkinson, the commander of U.S. forces in the area during the Black Hawk War (1832) against a mixed band of Sauk, Meskwaki and Kickapoo peoples. The city developed at the site of Fort Koshkonong, which was used during that war. A replica of the original 1832 stockade has been built just outside of town, although not at the original site. The fort was located to control the confluence of the Rock and Bark rivers.
The settlement grew rapidly in the mid-nineteenth century, after migration of United States pioneers from the East, especially from New York State and the northern tier. They were among the many migrants carrying the New England Yankee culture west across the northern tier of states.
The history and natural history of Fort Atkinson and the surrounding area are presented at the Hoard Historical Museum and National Dairy Shrine Museum. William Dempster Hoard founded the nationally distributed dairy farm magazine, Hoard's Dairyman, in Fort Atkinson in 1885. The museums include the Frank and Luella Hoard House, the Dwight and Almira Foster House, and the Knox Research Library and Archive. The Dairy Shrine portion of the complex portrays the past, present, and future of the dairy industry.
The oldest man-made features near Fort Atkinson are a cluster of prehistoric earthworks indigenous mounds located just south of town. In a curious honor, settlers named them the General Atkinson Mound Group. Thes mounds are a remnant of the Woodland Period within present-day Wisconsin. They are effigy and geometric mounds, different from the platform mounds at nearby Aztalan State Park, built by peoples of the Mississippian culture, which reached its peak about 1300 CE, had settlements throughout the Mississippi Valley and its tributaries, extending from central Illinois northward to the Great Lakes and also to the Southeastern United States. Materials were traded within the culture from the Great Lakes to the Gulf of Mexico. A long panther intaglio appears on an mound west of town, the last remaining intaglio in the state.
Fort Atkinson's 19th- and early 20th-century building history is preserved in the Main Street and Merchants Avenue historic districts. Other Registered Historic Places include the Fort Atkinson Water Tower, Panther Intaglio Effigy Mound, David W. and Jane Curtis House, Hoard's Dairyman Farm, and Jones Dairy Farm.