Founded in 1794, in brush arbor meetings, the church, located in Emanuel County, was first named Green Leaf but changed to Ebenezer in 1877. The first building was built in 1800, three miles from the present site. Lt. Reubin Thompson was the first pastor. This building was still standing in the 1980's. The building in use now was built in 1877. All the trees were home grown and cut by the members. The approximately 50 pews vary in length because each family used its own measuring device to make enough pews to seat all members of that family. The Reubin Thompson, R. S. Family Association honors the founder of Ebenezer and meets annually. The group is dedicated to the upkeep of the building, cemetery, picnic area, and grounds.
In the 1980s the church was on the Stillmore Charge. The church was designated a South Georgia United Methodist historic site in 1986.