Fort Atkinson is a city in Jefferson County, Wisconsin, United States. It is on the Rock River, a few miles upstream from Lake Koshkonong. The population was 12,579 at the 2020 census. Fort Atkinson is the largest city located entirely in Jefferson County, as Watertown is split between Jefferson and Dodge counties. Fort Atkinson is a principal city of the Fort Atkinson-Watertown micropolitan statistical area which is in turn a sub-market of the larger Milwaukee-Waukesha-Racine CSA.