Some station locations, not listed here, became part of the Hudson-Bergen Light Rail and the River Line, both of which were largely built along existing railroad rights-of-way. Since its inception, NJT has closed several stations and opened new ones reflecting infrastructure improvements and discontinuance or additions in service. Amtrak provides service in New Jersey along the Northeast Corridor (NEC) between Newark and Trenton and at intermediate points. Service from Atlantic City to Center City, Philadelphia is provided by one line separate from the rest of the NJT system, though SEPTA Regional Rail service connects Philadelphia and Trenton. The regional rail network, which serves the northern and central parts of New Jersey and Rockland and Orange counties in New York, radiates from Hoboken Terminal in Hoboken, Pennsylvania Station in Midtown Manhattan, and Pennsylvania Station in Newark.

Since 2009, NJT is a stakeholder in the state's ' smart growth' transit-oriented development initiatives, its transit hubs forming the basis for transit villages. Soon after its creation, NJT commissioned a survey of operating stations, 53 of which were eventually nominated and listed on the state and federal registers of historic places in 1984.

In January 1983 it took over operation from Conrail, which itself had been formed in 1976 through the merger of a number of financially troubled railroads and had been operating commuter railroad service under contract from the New Jersey Department of Transportation (NJDOT). NJ Transit Rail Operations (NJTR) was established by NJ Transit (NJT) to run commuter rail operations in New Jersey. NJ Transit Rail Operations provides passenger service on 12 lines at a total of 166 stations, some operated in conjunction with Amtrak and Metro-North Railroad (MNR).

New jersey transit map