Settlers began arriving in Elk Run during the early 1700s, and by the establishment of Hamilton Parish in 1730 several hundred people lived in this frontier village. A wooden chapel stood at this site by 1740, and in the 1750s it was replaced by a large brick church in the shape of a Greek cross whose foundation outline remains visible. Under British colonial rule, the church served as a governing and administrative body, while the village of the 1750s included a tavern, a blacksmith shop, and an ordinary and served as a stopover for travelers heading north or west as settlement expanded into what later became Fauquier County. Colonial militia in the French and Indian War and military forces during the Revolutionary War stopped at Elk Run for rest and supplies. As the village grew and agriculture flourished, a post office was established in 1803. The church, once the community's landmark, fell into disuse after the Revolutionary War and the separation of church and state, and after 1811 villagers gradually took its brick, wood, and stone to build their houses. By the outbreak of the Civil War, two copper mines operated in Elk Run, and Union patrols guarding the nearby north-south railroad line camped there and skirmished with local Confederate cavalry. By the early 1900s Elk Run was much smaller but still had three general stores, a tavern, and a post office; the post office closed in 1907 and moved to the Midland community farther north. A one-room school remained in use around 1925, and by 2000 only a small general store remained at the Elk Run crossroads.