This church was built to replace the earlier Lunenburg Parish lower church erected in 1732 and abandoned after the Revolution. The Anglican Church, established since Jamestowne, suffered from association with the Monarchy resulting in most churches falling into disuse.
St. John's exemplifies the resuscitation of the Episcopal Church in Virginia under the leadership of the Rt. Rev'd Richard Channing Moore, elected second bishop in 1814. He inspired such young men as the Rev'd George Washington Nelson who actively served to rebuild North Farnham, Cople, and Lunenburg Parishes as their rector. His remains lie buried outside this church.