Because of its proximity to Fairfax Station, the church saw significant conflict during the Civil War Era and was used as a field hospital. The pews in the church were destroyed during the war and replaced soon after. Although Confederate troops pushed Union forces back and occupied the city, Clara Barton and other nurses and doctors remained at their post and tended to the wounded even after Confederate troops captured Fairfax Station. A plaque honoring Clara Barton can be found on the side of the church that faces Route 123.
Very few alterations have been made to the original clapboard structure of the church. In the nineteenth century a vestibule, choir loft, and the new steeple were constructed. A two-story sacristy was built on the east end, and an upper loft was added to serve as a residence for visiting priests. Electricity was installed in 1927 but did not affect the exterior of the building.
The church is still functioning today. Primary services are held at a newly constructed, larger church in close proximity to St. Mary's. Mass is still conducted six days a week at the historic church. Owing to its appearance and long history, the church is highly sought-after for private events.