With expansion of settlement away from coastal areas in the early 18th century, there was a growing need for houses of worship to be located nearer to the homes of the settlers. In the spring of 1728, a frame chapel was constructed approximately two and one half miles west of here. The effort was led by Reverend William Becket, a Church of England missionary, who reported that the building was located "in the forest of Sussex" and was named for St. John the Baptist. Despite attempts to sustain it, the declining condition of the structure, an insufficient number of clergy, and the economic and political turmoil of the times, resulted in the abandonment of the old church around 1800.
After sporadic efforts to revive the congregation, the church was formally re-established in 1867. The present building was completed in 1877, and consecrated by Bishop Alfred Lee in June of that year. It was extensively remodeled in 1936, when a veneer of brick was added to the exterior. The adjoining Parish House was completed in 1941. St. John The Baptist Episcopal Church was listed in the National Register of Historic Places in 1980.