Waunakee Baptist Church started with home Bible studies and then began to meet in 1995 at the Waunakee Middle School under the direction of Rev. Leon Leeds (the then WFBC director). The church had a trailer and had to bring the pulpit, song books and everything every Sunday morning to set up for church. Eventually they purchased the old Winn funeral home on Main Street in Waunakee and did some remodeling and moved the church there. In 2013 they purchased their present building.
Waunakee Baptist Church is an independent Baptist church in Waunakee, Wisconsin. The pastor is Matt Abrahamson.