This church was organized in 1877, with thirty members meeting in a home. The members chose the name, Ebenezer, by ballot. The first building, a wooden frame, was erected in October 1877. In 1953, the present concrete block building was built. The church was a part of the Georgia Conference from 1940-1968, and during that time was host to the district meeting of the women. In 1972, the Coastal District of the North Georgia Conference merged with the South Georgia Conference. This church was placed in the Statesboro District on the Reidsville Circuit, and, in 1983, it was placed on the Nepsey-Warren Charge.
In the early 1990s, new pulpit furniture, carpet, central heat and air, and a PA system were added. In 1992, the church was Charge of the Year for the Dublin District. In October 1995, the church celebrated its 118th anniversary. During the late 1990s, handicap access was added, the roof repaired, and a stove and refrigerator purchased for the social hall annex. In the early 2000s, the church building was painted, evening services on the third Sunday of the month began and new pews installed. A children's ministry was begun in 2003. In 2009, a young adult choir was organized and the ceiling in the sanctuary and the doors and windows were painted.