Sponsored Topics. Waupaca is a city in Waupaca County in the state of Wisconsin. The population was 5,676 at the 2000 census. The city is believed to be named after Sam Waupaca (or Chief Wapuka) of the Potowatomi tribe. The city is located mostly within the Town of Waupaca, though it is politically independent. A portion extends west into the adjacent Town of Farmington and there is also a noncontiguous area of the city in the Town of Lind to the south.