Reverend W.C. Williams was appointed to come to the Union County town of Afton in 1854, with the first class held in January 1855 in a private home. As membership grew, services relocated to the school house, then the old courthouse building, before the first permanent building was erected in the present-day church parking lot. In 1903, the present church facility was constructed.

Membership grew in the 1960s, when the local Presbyterian Evangelical Church disbanded. The church shares a pastor with congregations in nearby Lorimor and Arispe.