The original church, built one block south of the present site, was consecrated in 1843 by Bishop Leonidas Polk. In 1861, the second Bishop of Alabama, the Rt. Rev. Richard H. Wilmer, was elected there. During the Battle of Selma, St. Paul's rector, the Rev. James Ticknor, was wounded and the senior warden, Robert Philpot, was killed. Union troops under Gen. James H. Wilson burned the original church April 2, 1865.
The cornerstone for the present building was laid in 1871. William M. Weaver donated the property for the building designed by the renowned New York firm of R.&R.M. Upjohn in the English Gothic Revival style. The first service was held Easter Sunday 1875. Many of the South's post war leaders were members of this parish including Lt. Gen. Joseph E Johnston, Lt. Gen Joseph Hardee, Maj. Gen. John H. Forney, Capt Catesby ap R. Jones, and Capt. Joseph Forney Johnston, who later served Alabama as Governor and U.S. Senator.
St. Paul's Episcopal Church was listed on the National Register of Historic Places in 1975.
In 1890 Bishop Henry M. Jackson was elected and consecrated here. In 1893 former vestryman John G. Murray was ordained deacon and in the following year priest in St. Paul's. Bishop Murray was the first elected Presiding Bishop of the Episcopal Church of the United States.
In 1900 St. Paul's own rector, the Rev. Robert W. Barnwell, was elected Bishop of Alabama. He was consecrated in St. Paul's and established Selma as his Episcopal Residence until his death. In 1924 the Cloister and Parish Hall were built with bricks from Old Cahawba. Selma artist Clara Weaver Parrish designed the focal point of the Parish Hall, the Wedding Feast of Cana. This stained glass window was executed by Tiffany and Company of New York.
One hundred years after the Civil War, the Civil Rights Movement once more placed Selma in the national spotlight. Jonathan Myrick Daniels, an Episcopal seminarian from New Hampshire brought discord to St. Paul's by bringing blacks to worship services forcing the Parish to evaluate its attendance policies. His activism led to his martyrdom in Hayneville later in 1965. He was commemorated by the Episcopal Church in 1991 and his statue now adorns Canterbury Cathedral.