During his term as rector of St. Paul's, 1812–1826, William Holland Wilmer was a major figure in the rebuilding of the Episcopal Church in Virginia in the aftermath of its disestablishment.

[4] In 1823, Wilmer obtained permission from the vestry to build at his own expense a small lecture room on church property at the corner of Pitt and Duke Streets.

A larger building in Gothic style was constructed on the same site in 1859 that was also used as a Sunday school, lecture hall and meeting place until its demolition in 1955.

In 1823, after the Bishop of Maryland withdrew support for the Education Society and an effort to found a seminary in Williamsburg had failed, Wilmer and the Rev.

[9] Wilmer was part of a three-person delegation that parleyed with British Admiral George Cockburn during the Burning of Washington to save Alexandria from destruction.

Though he traveled to Lexington, Virginia, where he remained for the duration of the war, due to ill health, he never served with Confederate forces, but instead took the oath of allegiance to the Union imposed by the martial law authority.

[13] Union troops occupied Alexandria immediately following the bombardment of Fort Sumter and the town remained subject to military occupation for the duration of the war, even after a loyalist Virginia government was organized in 1863.

[14] Because the prayer book service made distinct mention of both the executive and the legislative departments of the government, Episcopal clergy were exposed to embarrassment whenever any part of the territory of the Confederate States was occupied by Union forces.

Dr. Stewart proceeded without paying any attention to the interruption; but a captain and six of his soldiers, who were present in the congregation to provoke an incident, drew their swords and pistols, strode into the chancel, seized the clergyman while he was still kneeling, held pistols to his head, and forced him out of the church, and through the streets, just as he was, in his surplice and stole, and committed him to the guard-house of the 8th Illinois Cavalry.

One month later, on June 23, 1865, the vestry submitted to the Federal occupation force a statement of charges for repairs to restore the church to its former condition.

All of these events culminated in a visit from the Presiding Bishop of the Episcopal Church USA, the Most Reverend Katharine Jefferts Schori.

[26] The divergent liturgical practices within the Diocese of Virginia and the intensity of feelings engendered by that controversy in its time are now recognized by some as precedent for dealing with current rifts in a tolerant and civil manner without schism.

[29] Reconciliation within the Episcopal Church after the Civil War concluded was strained by the suffering and losses of life on both sides during that conflict, but helped to heal by mutual expressions of good will.

Ian Markham, priest associate and Dean, Virginia Theological Seminary, wrote in 2008 regarding the rifts in the Episcopal Church (United States) and the Anglican Communion arising from controversies in the previous few years.

The literalism of fundamentalist Christianity, as articulated by American Baptists in the early Twentieth Century, is out of place, they contend, in the Anglican tradition, "which embraces both faith and reason and a sense of proportion."

[37] The three equal arches in the St. Paul's façade that rise the full height of the building below the gable create a shallow porch, through which the church is entered.

The preaching space was to be open, unencumbered by piers and columns, with a central pulpit centered on the east wall with only an alcove behind for a chancel.

[40] As conceived by Latrobe, the interior of St. Paul's would afford all in the congregation an unobstructed view of a raised central pulpit in front of the altar.

At the instigation of the vestry and over Latrobe's strident objections, the builder constructed galleries on the north, south and west sides of the church.

[45] As a result of further change in liturgical emphasis to give the Eucharist a more central role in worship, the altar was moved in 1968 from the rear of the recessed chancel to its center.