The land was acquired by the federal government in 1900 upon the establishment of the Lake Merced Military Reservation, with the purpose of assisting in the coastal land defense for San Francisco Bay. The fort, renamed for Major General Frederick Funston in 1917, began to take shape during World War I, with the construction of barracks and a series of coastal batteries. The batteries were declared obsolete shortly after World War II, but Fort Funston later became a Nike missile launch site. The fort was inactivated in 1963 and eventually transferred to the National Park Service to be administered as part of the Golden Gate National Recreation Area.
The area is covered with a network of trails suitable for hiking or horseback riding, many of which descend via Dutch sand ladders to the beach. The beach is known for its magnetic sand, and the strong, steady winds make the cliffs overlooking the beach a popular site for hang gliding.
Fort Funston is the only area within the Golden Gate National Recreation Area where off-leash canine activity is allowed.