Mukwonago, WI. Online Offers. Mukwonago is a village in Wisconsin. As of the 2004 census, its population was 8,519. The village is located mostly within the Town of Mukwonago in Waukesha County, with a small portion extending into the Town of East Troy in Walworth County. Mukwonago is located at 42°51′52″N 88°19′50″W / 42.864557°N 88.330619°W / 42.864557; -88.330619 (42.864557, -88.330619).