The formation of the landscape dates back 130 million years to the Cretaceous Period. During that time the area was under the sea and heavy deposition of sediment occurred. The earth crust buckled in the region creating fault blocks. One of the fault blocks was elevated becoming San Bruno Mountain.

San Bruno Mountain is located in the area formerly occupied by the Costonoan Indian tribe. They practiced a hunting, fishing and gathering economy. One prehistoric Native American habitation site from this group has been found within the park's boundaries. Another has been located just outside it.

With the arrival of Europeans, this group was quickly integrated into the Spanish/Mexican Mission System. Under the mission system, the San Bruno Mountain area was used for cattle and sheep grazing.

With the independence of Mexico from Spain, ranchos and certain properties were granted. The grant of Rancho Canada de Guadalupe la Visitation y Rancho Viejo was granted to Jacob Leese in 1839. As late as 1869, surveys showed civilization completely surrounded the mountain's flanks, but no settlements were on it.

John Crocker acquired the property in the 1870's. It passed to the Crocker Land Company upon his death. In recent times the surrounding area has been developed for light industrial uses and mineral resources recovery. A quarry, located on the north base of the main ridge, was used for gravel extraction.

At the summit, remains of an old Nike Missile early warning radar site can be seen. This was used as a defensive system during the cold war. This radar, with others around the bay area, were used to detect approaching enemy aircraft and direct the missiles to their targets. Due to the ideal location, a number of radio and microwave transmitters can be seen today on the summit.