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NJ TRANSIT operates the state's commuter rail network. The rail system features 11 lines in three divisions. Customers can transfer between all lines, except Atlantic City Rail Line, at the new Secaucus Junction station. (The Raritan Valley Line requires an additional transfer at Newark Penn Station.)

The Hoboken Division (includes the MidTOWN DIRECT service on the Morris & Essex and Montclair-Boonton lines to and from Penn Station New York and lines operating to and from Hoboken Terminal on the Morris & Essex, Main/Bergen, Pascack Valley and Montclair-Boonton lines).

The Newark Division (includes the Northeast Corridor, North Jersey Coast, and Raritan Valley lines operating to and from Newark Penn Station, Hoboken Terminal, and Penn Station New York).

The Atlantic City Rail Line (operates between the seaside resort city and Philadelphia, serving points in between).
NJ TRANSIT also runs rail service to and from points in New York State on the Pascack Valley and Port Jervis lines under contract with the Metropolitan Transportation Authority. NJ TRANSIT's rail network provides links to the region's other transit systems. Transfers to the state's bus system are possible at many rail stations, while at Penn Station New York, connections are available to Amtrak, the Long Island Railroad, and the New York City subway system. At Trenton, riders can connect to SEPTA and Amtrak.

At NJ TRANSIT's Hoboken Terminal, transfers can be made to PATH trains between Hoboken, Jersey City, Newark, and midtown Manhattan; to Manhattan-bound ferry service; and to NJ TRANSIT's Hudson-Bergen Light Rail System. At Newark Penn Station, the state's busiest transit hub, connections to Amtrak, PATH and NJ TRANSIT's Newark City Subway are available. PATH can be used to connect with NJ TRANSIT's Hudson-Bergen Light Rail System. On South Jersey's Atlantic City Rail Line, connections can be made to Amtrak and SEPTA at Philadelphia's 30th Street Station.