St. John's congregation was founded in 1843 by a group of immigrants from the Rhine province of Hessen Darmstadt and the Bavarian Palatinate. They first gathered from services at a log church located in Section 26 approximately a half mile west of the present site. The original Historic Cemetery is still located there. In 1867 the congregation purchased three acres in Section 35 for the purpose of building a new church and parsonage. It was designed by the architectural firm of Myath & Koch and built by stone mason Peter Bronn. The stone was quarried from the land of members Conrad Dexheimer, Henry Leonhardt and Valentine Schaetzel. A new cemetery began next to the newly built church. St. John's also has the distinction of being a Washington County Landmark.
The church and its Historic Cemetery received Germantown Historic Designation in 2014