- Local/Commuter - The current operational service from Tutuban to Alabang, known as Metro South Commuter.
Other Routes: Tutuban-Calamba (suspended), Tutuban-Biñan, Tutuban-College, Tutuban-Santa Cruz (some services). Tutuban-Calauag, Mayao-Calauag.
- Rosal & Camia - Services between Tutuban and Santa Mesa to Guadalupe.
- Sampaguita & Ilang-Ilang - Services between Tutuban and San Pedro to Carmona with some trips originate from Caloocan.
- Bicol Commuter - Commuter Services on the Bicol Region, with some through trips to Quezon, the currently operational routes are Sipocot-Naga, Mantalisay Naga and Naga-Legazpi.
Other Routes: Hondagua-Naga, Tagkawayan-Naga, Ragay-Naga.
- Bicol Express - The Main Service between Manila and Legaspi, early services only reach as far as Aloneros until the Lne was completed in 1938.
- Bicol Semi Express - Services between Manila and Naga.
- Bicol Night Express - Services between Manila and Legazpi with Sleeper cars.
- Manila Limited - Services between Manila and Calauag in the early 1920s, also between Manila and Iriga as seen from 1988 and 1991 timetables.
- Southern Star and Cargo Express - The freight services of the PNR.
- Lucena Express - Services between Manila and Lucena and Malvar (Luta) to Aloneros.
- Batangas-Lipa Express - Services between Manila and Bauan.
- Peñafrancia Express - Introduced in 1986, this service between Tutuban and Naga only stops at Paco, more stations were added later.
- Kaunlaran Express -
- Mayon Limited - Services between Manila and Legazpi, introduced in 1967 as an faster alternative to the Bicol Express.
- Mayon Limited Special - Also known as Prestige, services between Manila and Legazpi but unlike previous services, it uses Motor Baggage Power railcars.
- Mayon Limited Ordinary - Services between Manila and Ligao using donated Kiha 52 railcars.
- Isarog Express - formerly known as Mayon Limited Deluxe, services between Manila and Ligao using Kiha "Kogane" 59 railcar.