South Prairie was platted in 1888 by Frank Bisson. It was named because of its location, south of Connell's and Porter's prairies. South Prairie was officially incorporated on February 17, 1909.
According to the United States Census Bureau, the town has a total area of 0.40 square miles, of which, 0.39 square miles is land and 0.01 square miles is water. It sits at an elevation of 430 feet above sea level.
South Prairie is located at 47°8′18″N 122°5′49″W (47.138402, -122.096848).