Fort Mason served as an Army post for more than 100 years, initially as a coastal defense site[3] and subsequently as a military port facility.

The Army recognized that the relatively small port facility at Fort Mason was inadequate for supporting major wartime operations in the Pacific.

In early 1941 the Army began acquiring land and facilities for major expansion in Oakland, Seattle and elsewhere in the San Francisco area.

[7][9][10] The shoreline of Black Point is the last remaining section of original coastline in San Francisco east of the Golden Gate Bridge.

[11][12] The nucleus of Fort Mason was a private property owned by John C. Frémont, the explorer of the western U.S., who also spearheaded the conquest of California from Mexico, and ran as the first presidential nominee of the extant Republican Party in 1856.

Appointed a major general in the Union army at the start of the Civil War, Frémont's repeated serious conflicts with President Lincoln led him to resign by late 1862.

Frémont would again contest the US presidency in 1864, running as the candidate of Radical Democracy Party, only resigning the effort when Lincoln fired a political enemy in his cabinet as a concession.

At that time, Frémont was still very preoccupied with enough of the vast fortune he had made through gold-mining before the Civil War that the matter was unlikely of concern to him; but by 1872[15] he was in grave financial trouble he would never escape before his death in 1890.

Initially these defenses were built as temporary wartime structures rather than permanent fortifications and one of these was constructed in 1864 at Point San Jose, as the location of Upper Fort Mason was then known.

Chaired by Secretary of War William Endicott, the board recommended new defenses at 22 U.S. seaports, deeming San Francisco Harbor second only to that of New York in strategic importance.

With these new facilities, Fort Mason was transformed from a harbor defense post into a logistical and transport hub for American military operations in the Pacific.

During World War II, Fort Mason became the headquarters of the San Francisco Port of Embarkation, controlling a network of shipping facilities that spread across the Bay Area.

[26] During the early months of the War, Lieutenant Ronald Reagan, US Cavalry Reserve, was assigned to a planning unit ("The Backroom Boys") commanded by Colonel Phillip T. Booker.

[23] The Korean War in the 1950s also kept the post busy, and in 1955 the San Francisco Port of Embarkation was renamed the U.S. Army Transportation Terminal Command Pacific.

A path follows the harbor edge, rising along the headland and offering views north past Alcatraz and west to the Golden Gate Bridge.

[30] The newest space is Gallery 308, whose inaugural exhibition was Janet Cardiff'sThe Forty Part Motet (November 14, 2015 – January 18, 2016), followed by Sophie Calle's Missing (June 22, 2017 – August 20, 2017).

From 2017 until its closure in 2022, the San Francisco Art Institute opened a graduate program campus, housed in FMCAC's historic Herbst Pavilion.

A proposal exists to extend the F Market & Wharves or E Embarcadero historic streetcar line to a terminal at Lower Fort Mason.

An Environmental Impact Statement for the extension, involving the San Francisco Municipal Railway, National Park Service and Federal Transit Administration, commenced in May 2006.