The original anchorage and clubhouse were located in San Francisco near Mission Rock, but inadequate depth of water and increasing industrial growth in the area resulted in a move to Sausalito.

Another group felt that the Club should move back to San Francisco and lease land from the city government on the Marina.

The San Francisco Yacht Club, with its tranquil setting in Belvedere Cove and its superb harbor, is widely recognized[by whom?]

[citation needed] It operates a year-round facility including the harbor, a dry sail area, a full-service restaurant, and a bar.

In July 2020, The SFYC built the Cove House, a facility that features both indoor and outdoor spaces in which members can host events, regattas, private parties and more.