The tunnel runs under Twin Peaks and is used by the K Ingleside, L Taraval, M Ocean View and S Shuttle lines of the Muni Metro system.

"[3] In April 1910, a committee, named the Twin Peaks Convention, was formed to plan the project, which would open the development of approximately one quarter of San Francisco's land area.

Market Street would be extended southwest in a straight line across private property to connect to the eastern portal, to be located at the intersection of 19th and Douglass.

5B, concluding "I can recommend unqualifiedly [sic] the construction of a Twin Peaks Rapid Transit tunnel at the earliest possible date.

In so doing, there will be brought within 30 minutes' running time of the business district, approximately 10,000 acres of new territory, 75% of which is suitable for residence land, that has been practically useless heretofore by reason of lack of adequate transportation thereto.

[8][9] The San Francisco Call speculated the presence of a station at Laguna Honda meant the Geary line could be extended through Golden Gate Park.

[10] A 1912 report, by Arnold, proposed that Laguna Honda would be a transfer point, enabling passengers to move from Third and Market to Ocean Beach within 25 minutes on an express car, assuming a Seventh Avenue surface line was built.

[15][16] With the addition of 15,000 acres (6,100 ha) of "the best residence property on the peninsula within 15 minutes of the business center of the city", the Call estimated the population of San Francisco would add 100,000 within three years and 200,000 within five.

Storrie Company for US$3,372,000 (equivalent to $102,570,000 in 2023)[1]: 5, 7  and work began on the Twin Peaks Tunnel in December 1914, with an estimated three-year construction schedule for the twin-track bore.

[22] The eastern 1,665-foot (507 m) portion (with the exception of the 300-foot (91 m) long Eureka Valley station) of the tunnel uses a double-tube subway structure, and the remainder adopts an arched tube profile.

[1]: 6  The lunette space between the arched roof and flat ceiling of the tube was used as a duct to convey fresh air into the tunnel.

[30][31] Mayor Rolph served as the motorman for the first revenue trip, and most of the paying passengers were City Supervisors, wives, and invited guests.

[34] When the Market Street subway was built in the early 1970s, it was connected to the Twin Peaks Tunnel to be used by the K Ingleside, L Taraval and M Ocean View lines.

The last Trolley Festival took place in 1987, and by the time its replacement, the F Market line, opened in 1995, its streetcars were able to use the J Church for "pull-in" and "pull-out" trips (to and from the carhouse)[36]: 86  because the 1991-opened extension of the J line from 30th Street to Balboa Park BART station had provided an alternative routing for streetcars traveling between Metro Rail Center (and the nearby Cameron Beach Yard) and Castro.

[37] Forest Hill and Eureka Valley stations were originally constructed with low platforms, as streetcars of that era had steps to load passengers from street level.

[38] On March 30, 2020, Muni Metro service, including trains through the Twin Peaks Tunnel, were replaced with buses due to the pandemic.

[40] K Ingleside and L Taraval services were interlined, running between SF Zoo and Balboa Park and not entering the tunnel, with passengers transferring at West Portal station.

[42] Service was stopped and substituted with buses just three days later due to a malfunctioning overhead wire splice in the subway and the need to quarantine a control center staff after a COVID-19 case.

[56] During the closure, Muni Metro trains were short turned at Castro station; the surface section of the K Ingleside was through-routed with the J Church, while the L Taraval and M Ocean View were replaced by buses.

[61] Muni was also criticized for inadequate notice of service degradation to bus lines during the closure, since buses were pulled off regular routes to substitute for trains,[62] and for the death during the project.

Muni had planned to replace the ballast, which degrades over time, creating a dust called fines, which can turn to mud when water enters the tunnel.

By November 2020, Muni acknowledged that it had made an "oversight" during the 2018 project and that the ballast was likely to create track stability issues in the Eureka Curve just west of Castro station.

Taking advantage of an unscheduled closure of the Muni Metro due to the COVID-19 pandemic, the agency replaced the ballast between November 2020 and February 2021.