St. John’s United Church of Christ has a long history, including the origins of the church in Eagle Valley near Fountain City, WI. St. John’s Church entered a shared covenant in 2021 with Hope UCC, and Pastor Deb Kunkel serves both churches. In 1870 the Swiss and German pioneers in Eagle Valley organized Emmanuel Evangelical and Reformed church. The congregation initially met in homes. In the late 1870’s while raising funds to build a church, worship services were held in the nearby Eagle Valley Public school. The first church was built and dedicated in 1892, located about 7 miles from Fountain City. A tornado in 1903 destroyed the wood frame church, and two years later was rebuilt using brick construction. Worship in Eagle Valley continued until 1949 when the dwindling congregation joined with St. John’s in Fountain City. St. John’s Evangelical and Reformed congregation was organized in 1886 in Fountain City, and the church was built the following year. The same pastor served both Eagle Valley and St. John’s. After the Eagle Valley congregation joined St. John’s in 1949, the growing membership and attendance resulted in building a new church in Fountain City in 1952. An educational wing was added to the church in 1968. Major remodeling of the sanctuary and a lift added for accessibility was completed in 1997. The Church in Eagle Valley was historically preserved and donated to St. John’s in 2003. Friends of Eagle Valley Community Church, an independent ecumenical committee, manages its use and maintains the restoration. As it is now named, this Community Church is available for any church to use for worship services, memorials, or weddings. In 2011 a pavilion with tables was added on the church grounds to accommodate gatherings of church or family.

The mission of St. John’s UCC seeks to establish and maintain within the local community, a Christian congregation to promote a life for worship, to advance the Kingdom of God by all means, both at home and abroad. Our church holds interfaith activities that are open and inclusive, seeking a balance between church and being active in community; examples being food shelf, prayer chain, bible studies, book reading group, and Habitat for Humanity. "St. John’s UCC is a community of people who, by God’s grace, are neighborly disciples with mission and purpose, who love others as Christ has loved us."

In 1957 St. John’s Evangelical and Reformed Church became St. John’s United Church of Christ as a result of a merger. The denominations of the Congregational Christian Church, along with Evangelical and Reformed Church joined to form United Church of Christ. UCC is a distinct and diverse community of Christians that came together as one church. They joined faith and actions and currently are over 5,000 churches with nearly one million members across the U.S. The UCC serves God in the co-creation of a just and sustainable world. The UCC is a church of "firsts," a church of extravagant welcome, and a church where "…they may all be one".