Wautoma is a city in Waushara County, Wisconsin, United States. The population was 1,998 at the 2000 census. Wautoma is the county seat for Waushara County.
The city consists of three noncontiguous areas: one is entirely within the Town of Wautoma, the second is entirely within the Town of Dakota, and the third straddles the boundary between the two towns.
According to the United States Census Bureau, the city has a total area of 2.5 square miles (6.6 km²), of which, 2.5 square miles (6.5 km²) of it is land and 0.04 square miles (0.1 km²) of it (1.57%) is water.