This church was organized on October 12, 1885. According to the 1918 Minutes of the South Georgia Annual Conference, Shiloh was on the Spring Hill Circuit in the McRae District with Rev. R. M. Dalton as pastor. By 1940, the McRae District was dissolved and Shiloh was assigned to the Alamo Circuit, Dublin District with Rev. Bill Kelly as District Superintendent. Rev. J. Frank Snell was pastor of the Alamo Circuit. In 1968, Browning, Shiloh, and Spring Hill formed the Wheeler County Circuit.
In 1990 stained glass windows were installed in the sanctuary. The Sunday school annex has been air-conditioned and painted. During the last several years the church has started a Bible Study, a music program, Fall Hay Rides, and Christmas gift basket deliveries. The parsonage was renovated in 2014. Also in 2014, the Shiloh Circle was established to help coordinate community activities and mission work for the church.