The building now known as St. Paul's Church was constructed between 1799 and 1801 for use as a district courthouse serving Fairfax, Fauquier, Loudon, and Prince William Counties. The original building design was so similar to that of the Fairfax County Courthouse, designed by James Wren, that its design has also been attributed to Wren.
The first court session was held in the district courthouse during the spring of 1803.
When the district court system was abolished in 1807, the building was put up for sale and purchased by the Hygeia Academy. The unprofitable school had to close its doors in 1816. The property remained unused until it was sold to William Skinker, Jr. in 1822.
In 1830 William Skinker, Jr. deeded the building, along with 1½ acres of land, to Leeds Parish for use as an Episcopal church in loving memory of his wife, Harriett Keith Skinker. Four years later, Bishop William Meade consecrated the building as St. Paul’s Episcopal Church.
From 1861 through 1865, the Civil War brought both sides of the battle to St. Paul’s at different times. Both the North and the South used the building as a hospital for the wounded and the grounds for burying the dead. In 1862 Union troops converted the building into horse stables before eventually burning it. Today there are markers dedicated to the memory of Union and Confederate soldiers buried on the church grounds.
The first minister to serve the church after the war was the Rev. William A. Alrich. In 1867 the congregation raised $600 to rebuild the gutted church. The first service in the renovated church was held on September 1, 1867. In 1881 The Diocesan Council created Haymarket Parish out of the original Leeds Parish.