- June 25, 1875 - King ALFONSO XII of Spain promulgates the Royal Decree directing the Office of the Inspector of Public Works of the Philippines to submit a general plan of railroad in Luzon
- February 5, 1876 - Don Eduardo Lopez Navarro of Public Works submits his MemoriaSobre el Plan General de Ferro-Carilles en Isla de Luzon, a very comprehensive and detailed study of railroad exploitation
- November 1, 1883 – the study of the first railroad project between Manila and Dagupandone by Antonio delaCamara isappoved
- January 1, 1887 – Royal Decree grants Mr. Edmund Syker the concession to the original plan as approved
- July 8, 1887 – the concession is transferred to Don Carlos E. Bertodano representing the Manila Railroad Company (MRRCo)
- July 31, 1887 – construction of the Manila-Dagupan railroad is started
- March 24, 1891 – the first section of the railroad from Manila to Bagbag (about 45 kms) is completed and put to commercial operations
- November 24, 1892 – the entire line from Manila to Dagupan, with a total length of 195.4 kms, is completed and put into commercial operations
- November 1896 – the Philippine revolution against the Spanish Government breaks out, interrupting railroad traffic at various points
- August 13, 1898 – the railway operations is resumed only to be interrupted again one year after when the Philippine-American War breaks out
- April 20, 1900 – the US military authorities returned the railroad to its owner
- July 1, 1902 – the US Congress authorizes the Philippine Government to grant franchise and concession for the construction of public utilities and services
- December 8, 1902 – the first Railroad Legislation Act (Philippine Commission Act No. 554) is passed granting the MRRCo the right to construct branch lines
- July 7, 1906 – Philippine Commission Act No. 1510 is enacted giving the concession of the railway to Speyer and Co. with Mr. Horace Higgins as General Manager
- February 4,1916 – By authority of Philippine Legislature Act No. 2574, former Governor General Harrison negotiates the acquisition of the MRRCo by the Philippine Government
- January 1917 – the acquisition of the MRRCoby the Philippine Government is consummated and the final transfer of ownership effected
- January 31, 1938 – the first Bicol train is put into operation
- May 8, 1938 – the unified system of railroad from San Fernando, La Union in the North to Legazpi in the South is formally inaugurated
- 1942 – 1945 – the railway comes under the control of the Imperial Japanese Army
- February 1, 1946 – the US Army restores the control of the railway to the Commonwealth Government
- 1954 – 1956 – Dieselization period of the railroad
- June 20, 1964 – Republic Act No. 4156 is enacted. It changes the corporate name of MRRCo to Philippine National Railways (PNR)
- August 20, 1971 – Republic Act No. 6366 is passed amending the PNR Charter
- January 26, 1973 – PNR is placed under the Civil Service Commission by virtue of PD No. 110
- July 3, 1975 – PD 741 is issued, providing for the strengthening of the financial structure of the PNR and expanding its role and participation in the total economic and social development of the country
- July 23, 1979 – by Executive Order No. 546, PNR becomes one of the attached agencies of the Ministry of Transportation and Communications, now DOTC
- August 23, 1989 – the Tutuban Station and part of the railroad yard is leased out for shopping mall development. PNR Management Center transfers to its Training Center site in Caloocan City and PNR Operations Center transfers to its railway station in Paco, Manila.
- February 2, 1992 – PNR inaugurates its first modern maintenance workshop in Caloocan. The workshop can accommodate 88 diesel rail car units at any given time
- February 22, 1992 – PNR acquires six (6) new DEL units from Japan thru the OECF loan
- June 1992 – the rehabilitation of the Main Line South Project funded by the OECF of Japan starts
- June 26, 1992 – PNR acquires an additional ten (10) new DEL units from Japan thru the OECF loan
- February 21, 1994 – President Fidel Ramos lays the cornerstone for the new Tutuban Terminal Building
- November 30, 1995 – Super typhoon Rosing heavily damages the tracks and bridges between Lucena and Naga, suspending train operations. The line is restored after one year.
- September 28, 2006 – Typhoon Milenyo damages San Cristobal Bridge and other PNR infrastructure in Quezon and Camarines Sur, resulting in the closure of line to long distance train operations
- November 30, 2006 – Typhoon Reming further damages the railroad infrastructure, particularly Travesia Bridge in the Ligao-Guinobatan section, and most of the station buildings and communication facilities
- December 22, 2008 – efforts start in the Reopening of the Bicol Line Project
- June 15, 2010 – President Gloria Macapagal - Arroyo launches the opening of San Cristobal Bridge
- June 29, 2010 – Train coming from Manila reaches Naga Station