Fort Madison is a city in and the county seat of Lee County, Iowa, United States along with Keokuk. Of Iowa's 99 counties, Lee County is the only one with two county seats. The population was 10,270 as of the 2020 census, and was estimated at 9,935 in 2025. Located along the Mississippi River in the state's southeast corner, it lies between small bluffs along one of the widest portions of the river. Fort Madison is also the home of the Iowa State Penitentiary.