Fort Atkinson is a city in Jefferson County, Wisconsin, United States. It is located on the Rock River, a few miles upstream from Lake Koshkonong. Money Magazine named Fort Atkinson 'One of America's Hottest Little Boomtowns'. The population was 11,621 at the 2000 census. Fort Atkinson apartments for rent comparison page shows most up to date rent information on Fort Atkinson apartments and houses. Rent information is obtained from multiple rental sources but we cannot guarantee their accuracy.