Now part of the Episcopal Diocese of New Jersey headquartered in Trenton, it was founded in 1706 by missionaries of the Society for the Propagation of the Gospel, London, England.

Thomas Bradbury Chandler led this congregation and helped found what became the Episcopal Church in the United States.

Following his Tory sympathies and fearing threats from the Sons of Liberty, Chandler fled to England in 1775, where he remained during the American Revolutionary War, only to accept the congregation's invitation and return to Elizabethtown and resume his duties during the last five years of his life.

Chandler forbad famed revival preacher George Whitefield from preaching in his pulpit during the winter of 1763–64[3] but did marry the parents of Elizabeth Ann Seton, who would become the first American-born Roman Catholic saint.

It once had five of the largest Tiffany stained glass windows in the U.S. Underneath is the unmarked burial site of the youngest signer of the U.S. Constitution, U.S.

St. John's has always been an ecumenical church and remains so today, but its governing body, the Vestry, is and was always composed of confirmed Episcopalians/Anglicans.