Shortly after the town of Waresboro was settled, there were Methodists gathered for services. In the early records, the preacher from the Waresboro Circuit preached at the beginning of the church in Waycross. In the Conference Minutes of 1842, Waresboro Mission is supplied by Seaborn Childs, in the St. Mary's District of the Georgia Conference. In 1845, it became a part of the Florida Conference until 1866, when those churches in the lower half of Georgia were returned to Georgia and the South Georgia Conference was formed. It was as part of the Waresboro Mission that the first services were held in Waycross. In 1888, this church was organized; Rev. J. G. Stern was the first pastor. There were seventeen members and they met in a new building. The present frame building was built in 1935 with the youth building being added in 1954. The inside has been remodeled and made comfortable. In 1919, the Waresboro Circuit had Waresboro, Fairfax, Millwood, New Prospect, Glenmore, Ruskin, and Axson; Rev. J. G. Hardin was the pastor. In 1940, it had Fairfax, New Prospect, Waresboro, Bickley, and Roxie Mae.
In 1964, the church became a station church. During the 1980s, the church purchased additional land for a parking lot; installed a stained-glass window, called the Good Shepherd, in the sanctuary, and had five active Sunday school classes, UMW, Men's Club, Golden Age Club and a young adult Volley Ball Team.