Public transit solely within the city of San Francisco is provided predominantly by the San Francisco Municipal Railway (Muni).

The city-owned system operates both a combined light rail/subway system (the Muni Metro) and a bus network that includes both trolleybuses and standard diesel buses.

The Metro streetcars run on surface streets in outlying neighborhoods but underground in the downtown area. Additionally, Muni runs the highly-visible F Market historic streetcar line, which runs on surface streets from Castro Street to Fisherman's Wharf, and the iconic San Francisco cable car system, which is the only moving National Historic Landmark in the U.S. Commuter rail is provided by two complementary agencies.

Bay Area Rapid Transit (BART) is the regional rapid transit system which connects San Francisco with the East Bay through the Transbay Tube.

The line runs under Market Street to Civic Center, where it turns south to the Mission District, the southern part of the city, and through northern San Mateo County, to the San Francisco International Airport, and Millbrae.

The Caltrain rail system runs from San Francisco along the Peninsula down to San Jose. The line dates from 1863, and for many years was operated by Southern Pacific.

The Transbay Terminal serves as the terminus for long range bus service (such as Greyhound) and as a hub for regional bus systems AC Transit (Alameda County), SamTrans (San Mateo County), and Golden Gate Transit (Marin and Sonoma Counties). Amtrak also runs a shuttle bus from San Francisco to its rail station in Emeryville.

A small fleet of commuter and tourist ferries operate from the Ferry Building and Pier 39 to points in Marin County, Oakland, and north to Vallejo in Solano County.