The San Francisco Peninsula in California separates the San Francisco Bay from the Pacific Ocean.  On its northern tip is the city of San Francisco.  Its southern end is part of Santa Clara County, including the cities of Palo Alto, Los Altos, and Mountain View. The Peninsula, used as a local geographic term, refers only to the parts south of, and excluding, the city of San Francisco.  It is roughly equivalent to the area served by the 650 area code, or to San Mateo County itself.  A couple of the aforementioned cities in the northern part of the county are considered to be suburbs of San Francisco, Daly City and South San Francisco in particular.  Parts of the peninsula on the bay side are sometimes referred to as the West Bay.

The east side of the peninsula is a largely densely populated area that includes portions of Silicon Valley. It forms a commuter area between San Francisco to the north and San Jose to the south. A number of major thoroughfares run north-south: El Camino Real (SR 82) and US 101 on the east side along the bay, Interstate 280 down the center, Skyline Boulevard (SR 35) along the crest of the Santa Cruz Mountains, and Highway 1 on the west along the Pacific. The Caltrain commuter rail line runs roughly parallel to the El Camino and Highway 101 corridors.

Three bridges—the Dumbarton Bridge, the San Mateo-Hayward Bridge, and the San Francisco – Oakland Bay Bridge—cross San Francisco Bay from the Peninsula. To the north, the Golden Gate Bridge connects San Francisco with Marin County

Along the center line of the Peninsula is the northern half of the Santa Cruz Mountains, formed by the action of plate tectonics along the San Andreas Fault. In the middle of the Peninsula along the fault is the Crystal Springs reservoir. Just north of the Crystal Springs reservoir is San Andreas Lake after which the famous geologic fault was named.

The San Francisco Peninsula contains a gamut of habitats including estuarine, marine, oak woodland, redwood forest, coastal scrub and oak savanna. There are numerous species of wildlife present, especially along the San Francisco Bay estuarine shoreline, San Bruno Mountain, Fitzgerald Marine Reserve and the forests on the Montara Mountain block.

The county is home to several endangered species including the San Francisco garter snake, the Mission blue butterfly and the San Bruno elfin butterfly, all of which are endemic to San Mateo County. The endangered California clapper rail is also found on the shores of San Francisco Bay, in the cities of Belmont and San Mateo.