The island of Luzon has been endowed with nature’s blessings but only slightly stirred by trade and commercial activity. The galleons that plowed the seas to and from Mexico offered some awesome sights to the Filipinos at that time. Under these prevailing conditions, the railroad was introduced as means of exploiting the untapped riches of the virgin island of Luzon.

On June 25, 1875, by virtue of royal decree of King Alfonso XII of Spain, required Inspector of Public Works of the Philippine Island to submit a general plan for the establishment of a railroad line in the island of Luzon. After five months of conscientious study, Don Eduardo Lopez Navarro, head of the Public Works Office submitted the plan called “Memoria Sobre el Plan General de Ferrocarilles en la Isla de Luzon.” The plan was granted for its implementation. On June 1, 1887, a concession for the construction of a railway line from Manila to Dagupan, Pangasinan was awarded to Don Edmundo Sykes of the Ferrocaril de Manila-Dagupan, the original corporate name of Manila Railway Company Ltd. of London.

On July 31, 1887, the cornerstore was laid at the present site of its main terminal building at Tutuban, Manila. Five years later, on November 24, 1892, the first 195 kilometer railway line from Manila to Dagupan in Northern Luzon was opened for operation.

On February 4, 1916, the Philippine Legislaturer passed Act. No. 2547 acquiring the then Manila Railroad Company (MRR). Construction of lines continued such that by 1940, the railway had been extended up to Legaspi, Albay in the South and to San Fernando, La Union in he north. Branch lines were constructed from Paniqui, Tarlac to San Quintin, Pangasinan; from Tarlac, Tarlac to San Jose, Nueva Ecija; from Bigaa, Bulacan to Cabanatuan City; from San Fernando, Pampanga to Carmen, Pangasinan; from College to Sta. Cruz, Laguna and from Sta. Mesa to Hulo in Mandaluyong.

The Second World War brought considerable damages to the system. The United States Army, which had temporarily gained control of the Company, after the war in 1945, was able to restore 40% of the pre-war lines.
On February 1, 1946, the control of the railway system was turned over to the Philippine Government. Of the 1,140 route-kilometers before the war, only 452 route-kilometers were made operational. Since then, the activities were concentrated on the rehabilitation and/or reconstruction of damaged railway facilities. The period 1954-1957 marked the dieselization program of the Company. Steam engines were retired and replaced by diesel electric engines.

On June 20, 1946, Republic Act No. 4156, the new Charter was passed, renaming the Company to what it is today – Philippine National Railways (PNR). This law had been amended twice: first Republic Act No. 6366 enacted on August 20, 1971 which provided for the rehabilitation and selective modernization program of the Philippine National Railways; and the second by Presidential Decree No. 741 issued on July 3, 1975 which raised the capital stock to P1.5 billion.

On July 23, 1979, Executive Order No. 546 was issued by the President of the Republic of the Philippines, creating the then Ministry of Transportation and Communications (DOTC), with the PHILIPPINE NATIONAL RAILWAYS as one of the attached government agencies.

In March 1990, the Main Line South (MLS) has been rehabilitated. The rehabilitation included the acquisition of Diesel Electric Locomotives (DEL) and the introduction of concrete ties in selected sections of the south line. In 1992, additional units of Diesel Electric Locomotives had been acquired.

On February 23, 1995, the Improvement and Modernization of Commuter Line South had been started. The Commuter Line South starts at Tutuban, Manila, and ends in Calamba, Laguna with branch line to Carmona, Cavite, a total stretch of 40 kilometers.