New Jersey
| New York Penn Station | Penn Station |
| Secaucus Junction | Opened on December 15, 2003. |
| Manhattan Transfer | Used from November 1910 until June 20, 1937. |
| Harrison | PATH station; moved to its current location on June 20, 1937, and previously served the Pennsylvania Railroad. |
| Newark Penn Station | |
| South Street (Newark) | Closed. |
| Newark Liberty International Airport | Opened on October 21, 2001. |
| North Elizabeth | |
| Elizabeth | |
| South Elizabeth | Closed. |
| Linden | |
| North Rahway | Renamed North Rahway from Scott Avenue circa January 1936; closed in 1993. |
| Rahway | |
| Colonia | Closed. |
| Iselin | Closed in 1972 after the opening of Metropark about a half-mile away. |
| Metropark | Opened on November 14, 1971, as Garden State Metropark. |
| Menlo Park | Closed 1957. |
| Robinvale | The depot was located near the Grove Ave. crossing. It closed in 1911, and the building burned in March 1915. |
| Metuchen | The first depot in this general vicinity opened in 1841. The current depot opened in 1888 and rededicated in 1979. |
| Lake Avenue | Operated from 1870 until 1888, when the new Metuchen station opened. The railroad razed the structure by looping a cable around it and attaching it to a locomotive. |
| Edison | |
| New Brunswick | |
| Jersey Avenue | Opened on October 24, 1963. |
| Princeton Junction | |
| Hamilton | Opened on February 16, 1999. |
| Trenton |
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