The Philippine National Railways used to provide passenger services in two directions from the capital, thus serving various towns and cities north and south of Manila. This list contains stations of both the North Main Line and South Main Line, and the various spur lines from both lines, as well as stations within Metro Manila. Former termini or terminal stations are in bold and former or defunct stations are in "italic".
North Main Line.
Stations along the Manila-San Fernando Line were abandoned and closed. San Fernando-Dagupan closed in 1983, Dagupan-Tarlac in 1988 and Tarlac-Malolos in 1989. The eruption of Mount Pinatubo further shortened services up to Meycauayan in 1991 until it was closed in 1997.
Bulacan.
The following stations were located in Bulacan with these closed between 1988 and 1991. A majority of these stations are being built under the North–South Commuter Railway (NSCR).
Pampanga.
The following stations of the North Main Line are located in Pampanga. Services here were closed in 1988 with some of the stations being built for the NSCR North's Phase 2.
Tarlac.
The following are the stations located in Tarlac. Stations south of Tarlac City were closed in 1988 while stations to the north were closed in 1984. There are no stations here planned for reactivation, with New Clark City being the only new station to be built as part of the NSCR.
East West Line (rapid transit).
The PNR East West line, or MRT Line 8, is a proposed rapid transit line in Metro Manila in the Philippines, generally running in an east–west direction along the Radial Road 7 and a portion of the Radial Road 8.
The line serves 11 stations on 9.4 kilometers (5.8 mi) of line. The rails are mostly elevated and erected either over or along the roads covered, with sections below ground. The western terminus of the line is the Hidalgo station infont of Quiapo Church along Quezon Boulevard, while the eastern terminus of the line is the UP Diliman station along Commonwealth Avenue in barangay U.P. Campus, Quezon City.
South Main Line (Southrail).
Albay.
[Abandoned because of a diversion line built by the PNR to alleviate the original high gradient, lava affected section between Camalig and Daraga]
Abandoned and inactive branches.
Abandoned.
Tarlac-San Jose branch.
An abandoned branch line serving Tarlac and Nueva Ecija. This line was also planned to be extended to Cagayan province, with services linking almost all the provinces in the Cagayan Valley. PNR has requested for a feasibility study for the revival of the line, to be connected to the North-South Commuter Railway project.
Santa Mesa-Antipolo branch.
Ceased operations when the San Juan River Bridge collapsed. Remains of the old railroad tracks from the old line are still present. The piers of the San Juan River bridge were still standing until they were demolished in 2018 due to the Skyway Stage 3 traversing through the river. It would be only feasible in the future to reactive just the Sta. Mesa-Mandaluyong parts of the line and the bridge rebuilt, with possible elevated tracks on the final segment to the Guadalupe station, which links the PNR to EDSA and MRT Line 3 (the nearest stations are the Guadalupe Station in Makati and Boni Avenue Station in Mandaluyong).
Balagtas-Cabanatuan branch.
This line is one of the branch lines that were abandoned after World War II. The line was reopened in 1969; however, it was once again left non-operational in 1980. If reactivated, it will serve thousands of people and tourists as well as provide freight services to the provinces of Bulacan and Nueva Ecija. PNR has requested a feasibility study for a planned revival as a northeast commuter line to Makati, as part of the process for getting the final nod on the project.
Rosario-Montalban branch.
An abandoned branch line which used to serve the cities of Pasig, Marikina, and the province of Rizal. This alignment is being proposed as a new spur line of the LRT-2 from the intersection of Munding Avenue and Marcos Highway in Marikina to original terminus in Montalban, Rizal with project name San Mateo railway.
Fort Stotsenburg-Dau branch.
A line from Fort Stotsenburg in Angeles to Mabalacat, Pampanga
Dau-Magalang branch.
An abandoned branch line from Dau to Magalang.
Nielson Field branch.
Abandoned after Nielson Field was closed.
Legazpi-Tabaco branch.
Abandoned line that served passengers and cargo going to Tabaco and its harbor.
Aringay–Asin branch.
This was a spur line meant to connect Aringay, La Union with Baguio. However, tracks actually terminated in Asin in Tuba, Benguet. Construction on the final section leading to Baguio was halted during World War I. The Salapak Tunnel, originally meant for the line, was used during World War II as the regional headquarters of the Imperial Japanese Army. During the PNR era, the right-of-way has been sold to residents and became either roads or farmland. The local government of Aringay also proposed to the PNR to convert the Salapak Tunnel into an ecotourism zone, but PNR turned down the request since there are plans to restore the tunnel in the future, referring to the PNR North Long Haul service.
San Fabian-Camp One branch.
This is a line to Camp One, Rosario, La Union. It was the first railroad project attempting to reach Baguio, abandoned however in 1914. A remnant is the triangle junction which was part of the rail tracks, which are now being used as roads.
Arayat-Carmen branch.
If reactivated, it would serve as a tourist line linking the PNR network to the Mount Arayat National Park and as a faster access to western parts of Pampanga, northern Bataan, southern Zambales and the Subic Bay Freeport Zone, with the possible construction in the future of a rail line linking the two economic zones, which would entail the building of a connector branch to link said line to the PNR system.
Tayug branch.
If reactivated, the line will serve residents and freight in Pangasinan, Nueva Ecija, and Tarlac, as well as help draw tourists to these provinces.
San Pablo-Malvar branch.
Branch line from San Pablo, Laguna to Malvar, Batangas. It was abandoned after the Los Baños to San Pablo route was built. If reopened, it would serve as an alternative to the main line.
Paniqui-Camiling branch.
Abandoned tram line that was operated by the Tarlac Railway Company.
Lingayen-Camiling branch.
Cancelled during the planning stages. The route was supposed to be from Lingayen, Pangasinan to Camiling, Tarlac.
Damortis-Tuba branch.
Branch line abandoned before the bed was completed and before any bridges had been constructed, the only remains of this line are the two railroad tunnels in Asin Road.
Caba-Galiano branch.
Abandoned before the bed was completed and before any bridges had been constructed
Paco-Naic branch.
Very few, if not none, of the original line exists today due to the path occupied presently by Ninoy Aquino International Airport and various developments since the line's closure.
San Pedro-Carmona branch.
This is the last branch line that was used by PNR up to early 2000s. In 2010, the land area of the station in San Jose (now considered on the tip and under the jurisdiction of GMA Cavite between San Pedro and Carmona), was allegedly re-leased to the private sector and the old rails were dismantled halfway up to Olympia Street in Pacita Complex. The old rails still exists from Chrysanthemum Station up to Crismor Ave. in Elvinda near the old San Pedro Station and is at least still in use by the squatter's trolleys. This line was opened in 1973.
Though inactive at present, PNR plans to reintroduce services to this branch line.
Cavite branch.
An abandoned branch line serving Cavite City and parts of Noveleta. 
The first section from Paco to Binakayan, Kawit opened on March 25, 1908 and Binakayan to Noveleta (including Caridad on the Cavite short line) on May 11, 1908. Naic Line started from Paco to Naic, Cavite. At Noveleta station, another spur line leads to Cavite City. Tanza to Naic section was opened in October 20, 1911 but ceased operations and abandoned in 1936. The rail tracks, including sidings between Las Pinas and Naic stations were removed in 1937 and in 1938, the reaming portion up to Paco was finally dismantled. Two bridges at Tanza, Cavite, and Brgy. Halayhay still exists but the tracks are gone.
The Naic line is a defunct line of the Manila Railroad Company.
The old PNR Tanza station still stands at 257 Tramo, Tanza, Cavite. It is a station on the defunct Naic line. The line from Salinas to Tanza (Santa Cruz de Malabon) in 1911 until 1936 cessation of services.
Pandacan-Isla Provisor branch.
Also known as the Santibañez line. This line had spurs leading to Isla Provisor, Luzon Brokerage Company, the closed Pandacan Oil Depot and the Johnson Picket Rope Company. It ends in what is now the Tabacalera Compound today. The bridge route's crossing in Pasig River is a mechanical swing bridge built to allow bigger ships to pass through. Today, not only is the mechanical component of the bridge nonfunctional, but the bridge itself cannot turn anymore due to the Pandacan Bridge built very close to its turning radius. The very bridge itself is still in use by trains, and occasionally by rickshaws and railskates. It is planned to be rebuilt as part of the NSCR South and the modernized Long Haul project to provide the PNR with a direct link to south central Manila.
Rongos branch.
A 1.7-kilometer line connecting the former Rongos wharf in the Bicol River for construction purposes. Dismantled after the completion of the South Line in 1938.
Inactive.
UP Los Baños-Santa Cruz branch.
This inactive line, when reactivated, could serve passengers and freight in the eastern towns of Laguna, while providing a faster access to tourist and historical destinations within the province.
Calamba-Bauan branch.
Part of the Long-Haul Railway project, it includes the construction of a new line to Bicol. The Calamba-Batangas City section of the branch will be reconstructed into a new single-track line that will be expanded to two when capacity is needed to be expanded.
Mamatid-Buntog branch.
This branch line, currently inactive, is the nearest rail link to the Nuvali residential township of Ayala Land, which extends to Calamba to the south, as well as to Tagaytay. It is also a potential branch line for a revived freight service from Metro Manila in the future, since a multimodal freight terminal was from the 1990s up to 2001 served by this line via container trains from the capital region.
Cabuyao branch.
The only remnant of this line is a railroad overpass crossing the South Luzon Expressway near Eton City Exit, claimed to be part of Cabuyao. The branch, if active, could have linked Eton City and the urban townships of Santa Rosa to the PNR system, as well as provide freight connections to the nearby industrial complexes and as a faster alternative to the Cavite-Laguna Expressway. Being located near Asian Brewery's facilities, it could also had been a direct connection there.
The Cabuyao branch was part of the Canlubang Estate rail network operated by the Canlubang Sugar Estate, which was linked to the PNR via its Canlubang branch line. This reveals that if so, the branch being connected to the PNR via the branch constituted a major link during the heyday of the sugar plantation, wherein its rail lines stretched northwards into Binan and southwards into Calamba. If revived today, that branch and others of the former CSE complex would have constituted an alternative to road transport options for the industrial complexes and the residential townships of 4 cities in SW Laguna which depend on the PNR.
References.
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