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.
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