Zion Lutheran Church resulted from a merging of two congregations.
Thompson Lutheran Church was organized in 1890, two years before the town of Thompson was incorporated. It joined the Evangelical Lutheran Synod in 1931.
The West Prairie Church was organized in 1875, and it joined the ELS in 1934.
In 1949, the Thompson and West Prairie congregations were combined to form Zion Lutheran Church in Thompson. The present church building was purchased from another congregation.
Zion Lutheran Church has shared pastoral services with Forest Lutheran Church in Forest City since 1945.
In 2024, Zion Lutheran Church and Forest Lutheran Church joined with Grace Lutheran Church in Lake Mills to form a three-point parish.