The San Francisco peninsula separates the San Francisco Bay from the Pacific Ocean. On its northern tip is the city of San Francisco and the Golden Gate Bridge leading over to the northern shores. On its southern end is part of Santa Clara County, including the cities of Palo Alto, Los Altos, Mountain View, and Sunnyvale. Most of the peninsula is covered by the entirety of San Mateo County. Locally, "the Peninsula" is used to refer to only the parts south of, and excluding, the city of San Francisco, roughly equivalent to the area served by the 650 area code, or sometimes to San Mateo County only.

A number of major thoroughfares run North-South: El Camino Real (CA-82) and Highway 101 on the east side along the bay, Interstate 280 (California) down the center, Skyline Boulevard (CA-35) along the crest of the Santa Cruz Mountains, and Highway 1 on the west along the Pacific. The east side of the peninsula is largely urban, forming a commuter area for San Francisco, San Jose to the south, Silicon Valley, Palo Alto and Stanford University.

Three bridges, the Dumbarton Bridge, the San Mateo bridge, and the San Francisco-Oakland Bay Bridge cross San Francisco Bay from the peninsula.

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, which inspired the James Bond movie, A View to a Kill. Just north of the Crystal Springs reservoir is the San Andreas reservoir after which the famous fault was named.