Waupun is a city in Dodge and Fond du Lac counties in the U.S. state of Wisconsin. The population was 11,340 at the 2010 census. Of this, 7,864 were in Dodge County, and 3,476 were in Fond du Lac County. In Fond du Lac County, there is also the Town of Waupun which abuts the city of Waupun.