The first congregation in this area was established in 1701 for the "upper inhabitants" of St. Peter's Parish. The congregation erected a Church in 1702 at a location now unknown, probably a few miles south of what is now St. Paul's. St. Paul's Parish was established in 1704. A larger Church was built in 1729 and used throughout the Revolutionary War. It was sold sometime after 1785 to another denomination and is now known as Slash.

Hanover Courthouse was built in 1735; it was probably the site of services in this area beginning around 1800. IN 1840, Bishop Richard Channing Moore laid the cornerstone of a brick church on the present site, within a short distance of the courthouse. The building was consecrated in 1845 with Bishop John Johns present. The current structure was completed in 1895, following the destruction of the brick Church by fire in 1893.

In 1994, both the National Register of HIstoric Places and the Virginia Historic Landmarks recognized St. Paul's as an historic landmark.