Thornton Gap was named for Francis Thornton (1711-April 14, 1749), owner of the land to the east and the "F.T. Valley." In 1740, he built a mansion in the Piedmont region near Nethers in Rappahannock County. The privately-owned Thornton's Gap Turnpike Company was formed to build a road over the mountains at Thornton's Gap. The toll road opened in 1806.

During the Civil War, the Great Valley of Virginia was known as the "breadbasket of the Confederacy" and so was the scene of intensive military action and much destruction. But the Blue Ridge Mountains witnessed only limited military actions and few depredations as the contending armies merely passed through on their way to larger confrontations.

Thornton was one of many passageways that led across the Blue Ridge. Two others were the Gordonsville Turnpike that crossed the Blue Ridge at Fishers Gap and Swift Run Gap Turnpike that crossed at Swift Run Gap. But when Skyline Drive was completed in the 1930s, the National Park Service chose to limit vehicular access to the mountaintop and closed the many roads that crossed the ridge. Today, many of these historic routes are maintained as fire roads or provide limited access for administrative purposes.

Prior to the building of Skyline Drive by the federal Works Progress Administration (WPA) during the Great Depression, the lost town of Beahm was located at Thornton Gap.