This hallowed ground, established December 12, 1884, by a general order signed by command of Lieutenant General Sheridan and Adjutant General R. C. Drum became the first West Coast cemetery to be part of the national cemetery system. The first interment was July 23, 1852 and it became a National Cemetery in 1884. This cemetery is closed to new interments.

On July 19, 1922, 38 bodies were unearthed in an isolated spot of the Presidio. The bones were believed the remains of early Spanish conquistadores who founded the local fortification. The bodies of 474 unknown dead sent here from early Western frontier camps and stations in the Philippine islands have been buried in one grave. In all, the National Cemetery lists 510 unknown bodies.