[6] Muni is the seventh highest-ridership transit system in the United States, with 142,168,200 rides in 2023, and the second highest in California after the Los Angeles County Metropolitan Transportation Authority.

Other passes and stickers are valid on all Muni lines, including cable cars, but not on BART (with the exception of BART-Plus[17] ticket types).

"Passports" are folding scratch-off passes that can be purchased by mail, or at various places throughout the city; they are good on all regular-service lines without surcharge, including cable cars.

The electricity to run all of Muni's trolleybuses, light rail vehicles, streetcars, and the cable car powerhouse comes from the hydroelectric dam at the Hetch Hetchy Reservoir in Yosemite National Park.

During World War II, because male employees had been called to serve in the military, both MSRy and Muni hired female 'motorettes' and conductors, including poet and author Maya Angelou in 1943.

Because it was assumed BART would provide local rail service, investment in Muni infrastructure failed to keep pace with major urban redevelopment projects.

Construction on BART's Market Street tunnel started in 1967,[104] with two decks tracks – the upper intended to provide local service.

Major cost overruns in the BART project forced the state legislature to rescue the project in 1969: curtailing local service in San Francisco and converting the partially constructed stations into the basis of a new light-rail subway called the Muni Metro to connect the downtown stations to the Twin Peaks Tunnel and continuing along reserved tracks to St. Francis Circle.

In September 1982, the cable car system was shut down for 21 months for rebuilding, and subsequent massive line reorganizations occurred to provide stronger cross-town services.

In 1983, Muni temporarily ran streetcars down Market Street as part of the San Francisco Historic Trolley Festival, initially conceived of as a substitute attraction for tourists during the one summer when no cable cars would be in operation.

[107] Anticipating the return of permanent streetcar service on Market Street, Muni began rehabilitating tracks in 1987, a process that culminated in the opening of the F line in 1995.

[108][109] In June 1995, the San Francisco County Transportation Authority released The Four Corridor Plan, a vision to extend Muni Metro service along four major routes in the city: Bayshore (north-south along Third from the county line to California), Geary (east-west along Geary from 48th to Market/Kearny), North Beach (extending the new north-south Bayshore line along Kearny and Columbus to Fisherman's Wharf), and Van Ness (north-south along Van Ness from 16th and Mission to Aquatic Park), with a connector downtown to transfer between the Bayshore, Geary, and North Beach corridors.

Automatic control of Muni Metro light rail vehicles began on Saturday, August 22, three years behind schedule and at a cost of $70 million, three times the original estimate.

Finally, riders who had previously been able to secure a seat by riding in the opposite direction (outbound) to Embarcadero station were forced to disembark there because of the E/Muni Metro Extension service that had begun in January; these changes and the delays frustrated many commuters.

[114] On Friday, August 28, 67 of the 131 LRVs (55 Boeing and 12 Breda) in the Muni Metro fleet were out of service for the morning commute; Mayor Brown personally rode from Civic Center to Embarcadero in the afternoon to experience the chaos for himself.

[115] Muni riders abandoned the underground system for carpools, taxis, buses, and F-Market streetcars after LRVs were delayed and stopped with no communication as to when they would resume service; transit times from 4th and Irving to Powell swelled to 120 minutes.

[116] On August 31, two San Francisco Chronicle reporters staged a 1+1⁄2-mile (2.4 km) race: one took the train, and the other walked along Market from Civic Center to Embarcadero.

[117] Mayor Brown re-enacted the race as the pedestrian on September 3; this time, Muni Metro service had improved and train passengers completed the trip in just seven minutes.

[118] At the request of the San Francisco Examiner, a member of the executive committee for Rescue Muni tracked the length of each ride on her eight-stop daily commute to the Financial District from the Sunset that week.

[121] Muni officials apologized for the rough transition and promised to continue to improve service;[122] privately they called the Meltdown "the biggest fiasco in the railway's history.

Construction on a sixth light rail line from Caltrain Depot in Mission Bay to Visitacion Valley and Bayview/Hunters Point was completed in December 2006.

Nathaniel Ford, executive director of Muni, said that the "marketing group has done an outstanding job making the key boarding areas more attractive and inviting for residents and our guests.

"[128] On November 15, 2007, city officials announced that they were looking into the possibility of adding double-decker buses to the Muni fleet, which would be operating mostly on the 38 Geary and the 14 Mission routes.

[129][130] On December 1, 2007, Mayor Gavin Newsom announced that the entire city fleet, including all of Muni buses, are henceforth powered with biodiesel, a combination of 80% petroleum diesel fuel and 20% biofuel, to reduce carbon emissions.

[138][139] Further improvements were made throughout the decade, amidst changes in both city and agency leadership, with the implementation of the "Muni Forward" project and all-door boarding.

[142] Infrastructure improvements include the addition of transit signal priority, bus bulbs, and bus-only lanes to more locations, and trackway repairs along the Muni Metro system.

[143] The 2010s also included the start of construction on bus rapid transit projects on Van Ness and Geary Streets[144][145] and the initiation of planning for new subway extensions that would potentially reach the Marina District[146] and Park Merced.

[160] A similar splice that failed in April 2019 in the Market Street subway between Powell and Civic Center disrupted services system-wide for more than 12 hours,[161] and led Mayor London Breed to seek a replacement for Muni head Ed Reiskin.

[186][187] The average speed of Muni vehicles has been slowly declining over the years due to increasing vehicular congestion and is now merely 8 miles (13 km) per hour.

The project was launched in a context in which twenty-five years had passed since the last comprehensive review, and travel patterns had changed, traffic congestion had increased, operating costs had risen and on-time performance had dropped since then.