The Town of Fountain Prairie is located in the southeast portion of Columbia County. It is bounded by Dodge County to the east, the Town of Columbus to the south, Town of Otsego to the east, and the Town of Courtland to the north. The Town covers approximately 22,397 acres of land, and had an estimated 2009 population of 878 people.
Fountain Prairie is primarily an agricultural community. Approximately 67.8% of the land in the town is utilized for agricultural purposes, while another 25.4% of the town is comprised of lands classified as woodlands and vacant or open space.