Waupun is a town in Fond du Lac County, Wisconsin, United States.
The unincorporated community of Ladoga is also located partially in the town.
According to the United States Census Bureau, the town has a total area of 35.0 square miles (90.6 km2), all land.
At the 2000 census there were 1,385 people, 472 households, and 407 families living in the town.
About 2.2% of families and 2.1% of the population were below the poverty line, including 1.0% of those under the age of 18 and 7.5% of those 65 and older.