Waupun is a city in Dodge and Fond du Lac counties in the U.S. state of Wisconsin. The population was 11,344 at the 2020 census. Of this, 7,795 were in Dodge County, and 3,549 were in Fond du Lac County. In Fond du Lac County, the Town of Waupun abuts the city of Waupun.

Dodge County is a county located in the U.S. state of Wisconsin. As of the 2020 census, the population was 89,396. Its county seat is Juneau. The county was created from the Wisconsin Territory in 1836 and organized in 1844.