Head of Apple Creek Church, was established first as an arm of South Fork of Mauvaisterre Church, through the efforts of Isaac Conlee and William Rodgers. It was organized as a separate church on the second Saturday in May 1828, but the other details of the constitution have been lost. Elder Isaac Conlee, a pioneer in this community, was one of the charter members, and served the church as pastor for nearly fifty years. He was buried in the cemetery on the tract where he settled, not over fifty feet from the place where the original log meeting house of Head of Apple Creek Church stood, about three miles south of Waverly. The church reported 19 members in 1828 at the meeting of the Sangamon Association.

In 1828, Head of Apple Creek Church united with the Sangamon Association; in 1830 the church became a charter member of the Apple Creek Association; and finally, in 1838, the church was a charter member of the Concord Association.

A second building, a frame structure, was later built on the James Stice farm, less than a mile northeast of the first. Services were held there until 1912, when a frame meeting house was purchased at Tanner and Kemper Streets in Waverly.

Pastors included Elders Isaac Conlee, W. J. Wright, A. W. Murray, C. C. Purvine, John A. Conlee, Elmer Sutton, Claud E. Webb, Baxter Hale, J. Bryan Adair, and James R. Harris.