This church was founded about 1869 by Mary Scott "Aunt Mary" Harvin, and held its first services in a nearby brush arbor. In 1881 church trustees purchased a one-half acre lot here from Dr. J.G. Dinkins for $35.00. The present church, built in 1901, was described as "enlarged and beautified on a very modern style" when two towers, a gallery, and anterooms were added in 1912.
This was one of several churches in Clarendon County to host meetings between 1949 and 1954 on the desegregation of public schools. On April 20, 1949, plaintiffs in the suit that became Briggs v. Elliott met here. That case was later part of the landmark decision in Brown v. Board of Education (1954). By late 2009 Rev. George P. Windley, Sr. was Ebenezer's longest-tenured pastor, serving more than 30 years.