The Metro North Commuter section ran from Tutuban to Governor Pascual station in Malabon and is colored light green in the system map of PNR.

On the other hand, the Metro South Commuter section ran from Tutuban to IRRI station in Los Baños, Laguna and was colored orange.

It temporarily closed on March 28, 2024 to give way for the construction of the North–South Commuter Railway (NSCR), which will assume its role upon completion around 2029.

Trains from Tutuban will lead to Naic in Cavite, Pagsanjan in Laguna, Montalban in Rizal, and Bulacan during the 1920s.

[8] The 100 km (62 mi) tram system reached Malabon to the north, Pasig to the east, and Libertad (now part of Pasay) to the south, making it one of the longest in Asia in 1924.

In 1976, the commuter system peaked and extended as far north as San Fernando, Pampanga,[10] Guadalupe (located in Mandaluyong on the other side of Pasig River) to the east, and College to the south.

Plans for expansion and rehabilitation such as the Manila–Clark Rapid Railway System project and Guadalupe line revival was also never realized.

[14] The Arroyo administration attempted to modernize the PNR system by rebuilding the lines and purchasing new rolling stock.

PNR purchased 6 brand new diesel multiple units from South Korea and became its first order in 35 years.

The project was financed by the Export–Import Bank of Korea and the Korean Economic Development Cooperation Fund[16] and was completed in 2010.

[18] PNR also acquired second-hand multiple units from Japan as stopgap measures to its train fleet, ending the Metrotren era.

[19] However, services were further suspended to Santa Rosa in 2014,[20] and to Alabang in 2015 due to safety issues and accidents on the line.

In 2017, the Department of Science and Technology announced its first Filipino-designed train and started trial services between Alabang and Calamba in 2018.

[26] In 2018, PNR acquired three diesel-hydraulic locomotives, 15 coaches, and six sets of diesel multiple units from Indonesian rolling stock manufacturer Industri Kereta Api (INKA).

The present line will also be rebuilt during and after the construction of the North–South Commuter Railway as it will serve as an alternate transport mode to the NSCR.

Prior to the line's closure, it terminated at Calamba Station despite having rails further towards Legazpi, Albay, but few trains stop at Sta.

During Holy Week, a public holiday in the Philippines, the line is closed for annual maintenance, owing to fewer commuters and traffic around the metro.

An automatic block signalling system by Mitsui was employed in the line as stated in a 1977 magazine by the International Railway Journal.

[3] On November 16, 2021, PNR published the bidding documents for the design, installation, and commissioning of the signalling, interlocking, and level crossing systems for the 29-kilometer (18 mi) Metro South Commuter section between Tutuban and Alabang.

Prior to the upgrade, the communications system backbone consisted of VHF radios, augmented with land and mobile phones.

The 12 series cars were hauled by PNR's diesel locomotives which were previously used in its intercity and freight services.

The agency then commenced the refurbishment of its entire fleet the following year, which introduced polycarbonate windows that can resist stoning as well as a new livery.

On July 2, 2023, regular MSC services were cut short to Alabang, following the closure of the line to Calamba.

On August 1, 2018, Philippine National Railways reinstated commuter train services to Caloocan station.

[6] Prior to the establishment of the PNR Metro Commuter Line, the Manila Railroad had several local train services in the 1950s and 1960s.

According to a timetable that was effected on August 16, 1954, local trains on the South Main Line from Manila reached Lucena station in Quezon province.

[46] After the intercity section of the North Main Line was closed in the 1980s, then-president Corazon Aquino inaugurated the resumption of commuter rail services to Meycauayan in Bulacan on May 10, 1990.

A spur line towards Carmona was opened on April 1, 1973, to serve the residents of the San Pedro–Carmona Resettlement Project.

Mesa, Buendia, Pasay Road, EDSA (flagstop), Sucat, Alabang, San Pedro, Biñan, and Santa Rosa.

On December 1, 2019, Train services to the International Rice Research Institute inside the campus of the University of the Philippines Los Baños were started.