[26] In 1978, at the request of the Philippine government, the Japan International Cooperation Agency (JICA) conducted a study on the electrification of the commuter service.

[29] On April 28, 1994, President Fidel Ramos signed an executive order designating Clark Air Base, a former American airbase, as the premier international airport, with the support of the Bases Conversion and Development Authority (BCDA), while the other agencies also supported the development, and in September of the same year, President Ramos signed a memorandum of agreement with Juan Carlos I of Spain for the construction of a railway line from Manila to Clark.

A joint venture agreement was entered into on June 10, 1995, between BCDA, PNR, Philippine companies DMCI Holdings and Fort Bonifacio Development Corporation, and Spanish firms with Construcciones y Auxiliar de Ferrocarriles, Entrecanales y Tavora, Cubiertas y MZOV, (both companies later merged to form Acciona) and Cobra Instalaciones y Servicios, S.A., as well as other investors.

The agreement also established the North Luzon Railways Corporation (NLRC) for the purpose of constructing, operating, and managing the railroad system on August 24.

Its initial phase involved the rehabilitation of the railway from Caloocan to Calamba and eventually the construction of spur lines to Carmona and Canlubang under a build–own–operate scheme.

[10] The contract between the NLRC and the Spanish Railways Corporation was terminated on August 14, 1998, after the parties disagreed on the source of funding for the project.

[8] Despite the contract termination, in September 1999, the National Economic and Development Authority (NEDA) approved the MCRRS, with the initial phase covering a segment from Caloocan to Calumpit.

[8] Then, JBIC later dumped the project because of the government could not commit to clear the railway path squatters before releasing a loan, causing a lack of funds.

Under the presidency of Gloria Macapagal Arroyo, the MCRRS was succeeded by the Northrail project, a 320-kilometer (200-mile) railway system from Caloocan to San Fernando, La Union.

[20] Its southern counterpart, the Southrail project, involved the rehabilitation of the entire South Main Line from Calamba to Legazpi, Albay, with an extension to Matnog.

[46][47] Meanwhile, the Northrail–Southrail Linkage involved the rehabilitation of the existing Metro Commuter Line from Caloocan to Calamba, creating a link between the two systems.

On September 14, 2002, a memorandum of understanding was signed by NLRC and China National Machinery and Equipment Group (CNMEG) for the project.

Senator Franklin Drilon commissioned a study from the University of the Philippines, which recommended the cancellation of the railway's construction, citing anomalies in the bidding process and the Buyer Credit Loan Agreement (BCLA) with Exim China.

On November 6, 2017, DOTr, BCDA, and NLRC reached an out-of-court settlement with Sinomach (formerly CNMEG), resolving the five-year dispute.

It saved the government ₱5 billion in potential payment of claims to Sinomach and hundreds of millions of pesos in legal fees and arbitration costs.

According to GCG, the company was "not producing the desired outcomes, no longer achieving the objectives and purposes for which it was designed and created, and not cost efficient and does not generate the level of social, physical and economic returns vis-à-vis the resource inputs.

[20] The government also examined building a railway on top of the North Luzon Expressway instead of using the PNR right of way, which was still allocated for the Northrail project at the time.

[55] On February 16, 2015, the NEDA board, chaired by President Aquino, approved the NSCR Phase 1 as part of the North–South Railway Project (NSRP).

[65][66] The NSCR, a part of the NSRP north line's first phase, was a 37-kilometer (23-mile) electrified narrow gauge commuter railway from Tutuban to Malolos, funded through overseas development assistance.

[67][68] Other components of NSRP masterplan include the reconstruction of the existing Metro Commuter line and the reestablishment of long-haul services to northern and southern Luzon, all of which were to be funded through a public–private partnership (PPP) scheme.

[70][71][72] Before the inauguration of President Rodrigo Duterte, Aquino's successor, Chinese diplomats reportedly offered to construct the railway from Manila to Clark within two years.

[74] On June 25, 2017, transportation secretary Arthur Tugade unveiled the locations of the first five stations during a press tour of the old PNR line.

[117] To fast-track the construction of NSCR South, the rest of the Metro Commuter Line services temporarily closed on March 27, 2024.

The first is the 91-kilometer (57-mile)[123] fully-elevated PNR Clark which is being built over the mostly-defunct North Main Line in northern Metro Manila and Central Luzon.

[131] The PNR has also requested for a feasibility study for a commuter line connecting Tarlac City and San Jose, Nueva Ecija in 2019.

[133] The North–South Commuter Railway will also have provisions for infill stations: Malabon, Valenzuela Polo, Tabing Ilog, Tuktukan, and Malolos South.

[137] A total of 464 electric multiple unit traincars have been procured to operate on the line, with 408 of these being the 8-car EM10000 class trainsets to be built by the Japan Transport Engineering Company (J-TREC), successor to the Tokyu Car Corporation that provided rolling stock to the Philippines from 1955 to 1976.

[139] The procurement for the 56 airport express trainsets began on February 26, 2021, with a suggested preliminary design based on the E259 and E353 series being published on the same day.

[140] After several months of delays and rescheduling, three bidders have submitted their designs on October 15: Kawasaki Heavy Industries and Sojitz, Marubeni and Stadler Rail, and Mitsubishi and Construcciones y Auxiliar de Ferrocarriles (CAF).

[150] The Banlic depot will be located on a 24.5-hectare (61-acre) lot in Calamba, Laguna, near the namesake barangay and station in Cabuyao, featuring a control center, stabling yard, maintenance shop, and ancillary buildings.