St. John's roots date back to 1739 when its members were a part of the church of the Swatara. The church was located about halfway between Williamsburg (Jonestown), and Stumpstown, (Fredericksburg) and the congregation of the Swatara Church separated into two divisions in 1765. One division went to Fredericksburg and founded a union church consisting of Lutheran and Reformed congregations. The other division came to Jonestown and received a grant of two lots from William Jones on South Broad Street, and together with the Lutheran people of the community, built a union church. The ground upon which the new church was built was subject to a ground rent of one red bean per year.
The Lutheran and Reformed Congregations worshiped together in the union church until 1804. That year, the Lutherans sold their interest to the Reformed Congregation and withdrew to build a church of their own. The Reformed Congregation continued to worship at that location until 1810 when a new church was erected on South King Street on the site of the present day Reformed Cemetery.
In 1851, the congregation decided to again build a new church. The cornerstone laying for this new house of worship was Saturday, September 27, 1857. The present congregation continues to worship in this church building at 120 West Market Street in Jonestown, Pa.
