San Pedro (then San Pedro Tunasan) was opened on August 1, 1908.
The station was renovated in 1972 for the opening of the Metro Manila Commuter Service which started operating on November 30 of the same year, the Carmona Line which branches from San Pedro was opened on April 1, 1973.
A new station located west of the old station was opened in 2013.
- Manila Railroad Company (Philippine National Railways today) has two San Pedro stations, the other one is the rubble stone flag station located in Brgy. San Pedro, San Quintin, Pangasinan, to distinguish this station from its original name San Pedro Tunasan or S.P. Tunasan, it is named San Pedro, Laguna or SPL.