Among those displaced persons from Charleston was the Reverend W. B. W. Howe, rector of St. Philip's Church, who with his family was staying at Mars Bluff. Mr. Howe, later Bishop of the Diocese of South Carolina, conducted services. Christ Church, Mars Bluff, established 1856, offered the new Episcopal congregation its support and guidance.

During 1867, the Reverend Walter C. Guerry, ordained a deacon on June 24 (St. John the Baptist Day), was assigned to organize a mission. On July 17 he was placed in charge of both a mission in Florence and one in Marion, S.C.

On July 28, Mr. Guerry preached his first and only sermon at the Florence mission, taking his sermon text from the gospel according to St. John. Shortly thereafter, he became ill and died August 15. Tradition holds that the Florence parish was named St. John the Evangelist as a memorial to its first priest.

On November 24, Mr. Guerry's brother, the Reverend L. F. Guerry, took charge of St. John's and the Church of the Advent, Marion.

In 1871, the first church building, at the corner of Darlington and Coit Streets, was consecrated.

In 1886, extensively damaged by earthquake, the building was abandoned and services were held in a hall over a store at the corner of Evans and Dargan Streets.

During 1887, the mission became a self-supporting parish.

Designed by Silas McBee and built of stone from Anson Quarries, Wadesboro, N.C., the present building was occupied in December 1889. Its first service, held December 22, included ordination to the priesthood of the Reverend W. A. Guerry. St. John's was the only parish of which he was the rector before becoming Bishop of the Diocese of South Carolina in 1908.

The present church building was completed in 1890.

On February 15, 1891, Bishop W. B. W. Howe consecrated St. John's new building. It was Bishop Howe who had conducted its first service in 1865.

During 1922, the parish house was built as a memorial to Mrs. Frances Church.

In 1957, the congregation established a new church, All Saints', located on Cherokee Road. The church building was extensively renovated in 1966, including additions to the Parish House.

In 1972, a new youth building was completed. In October 2001, the first phase of extensive renovations was completed. During his annual visit for confirmation, Bishop Skilton blessed the new fellowship hall, library, kitchen, and outdoor gathering space; an extensively renovated youth building; and the Poynor Room, which also underwent extensive renovations at the hands of the Episcopal Church Women organization. Additional renovations will follow over the next year. These will include painting and reflooring the parish hall, converting the old library into a chapel, and replacing the flooring in the choir room.