St. John's Protestant Episcopal Church may refer to:

St. John's Protestant Episcopal Church (Stamford, Connecticut), listed on the National Register of Historic Places in Fairfield County, Connecticut St. John's Protestant Episcopal Church (Baltimore, Maryland), listed on the National Register of Historic Places in Baltimore County, Maryland St. John's Protestant Episcopal Church (Yonkers, New York), listed on the National Register of Historic Places in Westchester County, New York St. John's Protestant Episcopal Church (Charleston, South Carolina)