Located in Germany Valley, Pendleton County, Schoolhouse Cave is found in middle Ordovician limestones along the crest of the Wills Mountain Anticline. Early accounts refer simply to "the large cave in the Harman Hills." The modern name was derived from the nearby oneroom Cave School, which closed in 1945.

During the Indian and Revolutionary wars the occupants of Hinkle's Fort used the cave as a source of niter (or saltpeter), the primary ingredient in the manufacture of gunpowder. The most intensive niter mining operation probably occurred during the War of 1812. At some point the miners constructed scaffolding and a tramway across the entrance room to the high passage containing the niter-bearing cave earth. Schoolhouse is the only niter cave known to have been worked by Unionists during the Civil War.

Before November 1939, no explorer had penetrated beyond the "Jumping Off Place," about 600 feet into the cave, where the floor drops away into a deep pit. The final 1,000 feet, a series of formidable pits and traverses, was explored by rock climbers of the Potomac Appalachian Trail Club during numerous expeditions from February 1940 to March 1941. During 1942, the daunting task of surveying the cave was completed. Although more challenging caves would be discovered subsequently, into the 1950s Schoolhouse retained its reputation as "the toughest cave" in the nation. In 1999, the large entrance was gated, prohibiting entry to conserve colonies of endangered and federally protected Virginia big-eared bats. The massive cave gate is one of the largest in the country.