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Commuter rail service in Philadelphia, Pennsylvania, US
Of the 13 branches, six were originally owned and operated by the Pennsylvania Railroad (PRR) (later Penn Central), six by the Reading Company, while one was constructed under SEPTA in 1985. The PRR lines terminated at Suburban Station; the Reading lines at Reading Terminal. The Center City Commuter Connection opened in November 1984 to unite the two systems, turning the two terminal stations into through stations. Reading Terminal was replaced by the newly built underground Market East Station (now Jefferson Station). Most inbound trains from one line continue on as outbound trains on another line. Some limited or express trains, and all trains on the Cynwyd Line, terminate on one of the stub end tracks at Suburban Station. Service on most lines operates from 5:30 a. m. to midnight.

YearMakeModelNumbersTypeTotalTare(Ton/t)SeatsNotes1973–76GE[[GE Silverliner IV101–188married pairs8862.5/56.8125Ex Reading304–39995Ex Penn Central417–46044Units renumbered when PCB transformers were replaced with silicone transformers.276–303single cars28Unit 280 repainted to Reading heritage livery400–41616Units renumbered when PCB transformers were replaced with silicone transformers.2010–13RotemSilverliner V701–738single cars3862.5/56.8110Replacements for 70 older Silverliner II and Silverliner III cars; will also add capacity. Deliveries were to begin in July 2022. After multiple delays, the order has been cancelled as of April 2024. Trailers34139

YearMakeModelNumbersTotalHpTare(Ton/t)Notes2018Siemens[[Siemens ACS 64901–915158,600107.5/97.6Entered service on July 11, 2018. Replaced [[EMD AEM 7 and [[ABB ALP 44 fleet.

All lines used by SEPTA are electrified with overhead catenary supplying alternating current at 12 kV with a frequency of 25 Hz. The system on the former PRR side is owned and operated by Amtrak, part of the electrification of the Northeast Corridor. The electrification on the Reading side is owned by SEPTA. The Amtrak system was originally built by the PRR between 1915 and 1938. The SEPTA owned system was originally built by the Reading starting in 1931. The two systems are not electrically connected. After construction of the Center City Commuter Connection, the two electrical systems now meet near Girard Avenue at a “phase break,” a short section of unpowered track, which trains coast across. The gap is necessary because the two electrical systems are not kept in synchronization with each other. The entire system uses 12 kV / 25 Hz overhead catenary lines that were erected by the PRR and Reading railroads between 1915 and 1938. All current SEPTA equipment is compatible with the power supplies on both the ex PRR (Amtrak supplied) and ex Reading (SEPTA supplied) sides of the system; the "phase break" is at the northern entrance to the Center City commuter tunnel between Jefferson Station and Temple University Station.

SEPTA was created to prevent passenger railroads and other mass transit services from disappearing or shrinking in the region. Passenger rail service was previously provided by for profit companies, but by the 1960s the profitability had eroded, not least because huge growth of automobile use over the previous 30 years had reduced ridership. SEPTA's creation provided government subsidies to such operations and thus kept them from closing down. For the railroads, at first it was a matter of paying the existing railroad companies to continue passenger service. In 1966 SEPTA had contracts with the PRR and Reading to continue commuter rail services in the Philadelphia region. The PRR electrified the Paoli line in 1915, the Chestnut Hill West line in 1918, and the Media/West Chester and Wilmington lines in 1928. Both railroads continued electrifying lines into the 1930s, replacing trains pulled by steam locomotives with electric multiple unit cars and locomotives. PRR electrification reached Trenton and Norristown in 1930. Reading began electrified operation in 1931 to West Trenton, Hatboro (extended to Warminster in 1974) and Doylestown; and in 1933 to Chestnut Hill East and Norristown. The notable exception was the line to Newtown, the Reading's only suburban route not electrified. While the PRR expanded electrification throughout the northeast (ultimately stretching from Washington, D. C. to New York City), the Reading never expanded electric lines beyond the Philadelphia commuter district. Bethlehem Quakertown service ended July 1, 1981, and Quakertown–Lansdale service ended July 27, 1981. Pottsville line service to Pottsville via Reading and Norristown, also ended July 27, 1981. West Trenton service previously ran to Newark Penn Station; this was cut back to West Trenton on July 1, 1981, with replacement New Jersey Transit connecting service continuing until December 1982. The final service, Fox Chase Newtown service, initially ended on July 1, 1981. It was re established on October 5, 1981, as the Fox Chase Rapid Transit Line, which then ended on January 14, 1983. Service from Cynwyd was extended to a new high level station at Ivy Ridge in 1980, and the 52nd Street Station closed in the same year.

The 1980s and 1990s were difficult times for SEPTA. While the agency has spent most of its 50 year history staggering from crisis to crisis, the 1980s were a particularly low point. The era was defined by crippling strikes, engineer shortages, drastic service cuts and an abundance of mismanagement. State and local officials, commuters, and general observers were quick to brand SEPTA as the most inept of all the major transit agencies, though getting a handle on what exactly was the cause of its ills was historically difficult. Railpace Newsmagazine contributor Gerry Williams commented that understanding what routinely transpires in SEPTA upper management rarely made itself clearly known to the general public. Frequently, there were various hidden agendas working in the background, often working at cross purposes with one another. This was often the result of the city (Philadelphia)/Suburban (Bucks, Delaware, Chester, Montgomery) split. The city government had historically been Democratic, the four suburban counties Republican until 2019, when all four suburban counties elected Democratic leadership. This factor is regularly influenced by the changing political winds at the state capital in Harrisburg. Service to Cynwyd ended altogether in 1988, but fierce political pressure brought resumed service. R8 diesel service between Fox Chase and Newtown ended on January 14, 1983, after SEPTA decided not to repair failing diesel train equipment. SEPTA management was criticized for the cuts. Vukan Vuchic, the transit expert and University of Pennsylvania professor who designed the former R numbering system for SEPTA, said he had never seen a city the size of Philadelphia "cut transit services quite as drastically as SEPTA. For a system that is already obsolete, any more cutbacks would be disastrous—and likely spell doom for transit in the Philadelphia region. This city would be the first in the world to do that." DVARP said that SEPTA purposely truncated service and that while other commuter railroad counterparts "in North America expand their rail services, SEPTA is the only one continuing to cut and cut and cut. The only difference between SEPTA and its railroad and transit predecessors is that SEPTA eliminates services to avoid rebuilding assets, while its predecessors (PRR, Reading and Conrail) kept service running while deferring maintenance."

On June 14, 2014, a strike shut down SEPTA's Regional Rail service after negotiations failed between SEPTA and the Brotherhood of Locomotive Engineers and Trainmen and the International Brotherhood of Electrical Workers. A total of 400 workers walked off the job. As a result of the strike, SEPTA planned to add additional capacity on bus, subway, and trolley routes along with the Norristown High Speed Line during off peak hours.

SEPTA Regional Rail operated "Lifeline Service" during the COVID 19 pandemic. On April 9, 2020, service was suspended on the Chestnut Hill East, Chestnut Hill West, Cynwyd, Manayunk/Norristown, West Trenton, and Wilmington/Newark lines. Service along the Lansdale/Doylestown and Paoli/Thorndale lines were also truncated to and , respectively. The West Trenton Line and Paoli/Thorndale Line service to resumed on June 15, 2020. Lansdale/Doylestown Line service to resumed on June 22, 2020. The Chestnut Hill East, Manayunk/Norristown, and Media/Elwyn lines resumed on June 28, 2020. On the same date, service levels increased on all lines except the Chestnut Hill West and Cynwyd lines. Service on the Chestnut Hill West Line resumed on March 8, 2021, on a limited schedule, with service running Monday through Friday. Service on the Cynwyd Line resumed with limited operations on September 7, 2021. Weekend service on the Chestnut Hill West Line was restored on December 19, 2021.

In February 2021, the city government of Philadelphia announced the Philadelphia Transit Plan, which outlines the city's proposals for its public transportation system through 2045. For Regional Rail, the plan included increased service frequency, a fare system overhaul, and the creation of many metro like Regional Rail lines within the Philadelphia city limits and close suburbs. Regional Rail would be split into the Silver Line, frequent Regional Rail (metro style lines), and Regional Express Service (lines similar to the current Regional Rail, which would make fewer stops closer to Philadelphia). This plan would require upgraded tracks and stations, new vehicles, and infrastructure replacement and upgrades. Similar to other major infrastructure upgrades to existing commuter networks such as GO Transit Regional Express Rail in Toronto or the Electrification of Caltrain in San Francisco. The plan also proposed extensions of Regional Rail services to Phoenixville, Quakertown, and West Chester. The 2045 Transit Plan breaks this into 3 phases.

Phase 1 entails the creation of the "Silver Line". The name comes from the Silverliner family of EMUs which are used in Regional Rail service, and was chosen to denote the metro like similarities between the Silver Line and the Blue (Market–Frankford) and Orange (Broad Street) lines. The Silver Line would run from Fern Rock Transportation Center in North Philadelphia to Penn Medicine station in University City. It would have the same frequency as a bus line, with 15 minute headway for 15 hours a day every week. Fares along the Silver Line would be similar to SEPTA's other transportation modes, including bus, trolley, and subway.

Phase 2 would include the addition of more metro like regional rail routes. These would be called Frequent Regional Rail lines and would be similar to the Silver Line, having lower fares, free transfers, and increased frequencies. Currently, there are four phase 2 routes proposed, including conversion of the Manayunk/Norristown, Chestnut Hill East, and Airport lines to Frequent Regional Rail, and a portion of the SEPTA Main Line from Fern Rock Transportation Center to Jenkintown–Wyncote station in Jenkintown would have Frequent Regional Rail alongside Regional Express Services.

Phase 3 would include the implementation of the final Frequent Regional Rail lines, additional infrastructure, vehicle, and station upgrades. As part of phase 3, the Chestnut Hill West, Fox Chase, and Warminster lines would be completely replaced with Frequent Regional Rail, while the Lansdale/Doylestown, Media/Wawa, Paoli/Thorndale, and West Trenton lines would have Frequent Regional Rail run alongside Regional Express Services to Lansdale, Elwyn, Villanova, and Somerton respectively. The city of Philadelphia and SEPTA expect this plan to take decades and billions of dollars to complete.