Common carriers

• Amtrak (AMTK) [1] (federally owned by the National Railroad Passenger Corporation)
• Belvidere and Delaware River Railway (BDRV) [2]
• Black River and Western Railroad (BRW) [3]
• Canadian Pacific Railway (CP) [4] (via trackage rights)
• Cape May Seashore Lines (CMSL) [5]
• Conrail (CSAO, formerly CR) [6]
• CSX Transportation (CSXT) [7] (Baltimore Division)
• Durham Transport (DRHY)
• East Jersey Railroad and Terminal Company (EJR) [8]
• Morristown and Erie Railway (ME) [9]
• New Jersey and Northern Railway (?)
• New Jersey Rail Carriers (NJRC?) [10]
• New York Cross Harbor Railroad Terminal (NYCH) [11]
• New York and Greenwood Lake Railway (NYGL)
• New York, Susquehanna and Western Railway (NYSW) [12] (commonly called the Susquehanna)
• Norfolk Southern Railway (NS) [13]
• Port Jersey Railroad (PJRR) [14]
• Raritan Central Railway (RCRY)
• SMS Rail Service (SLRS) [15]
• Southern Railroad of New Jersey (SRNJ)
• Winchester and Western Railroad (WW)

Commuter railroads

• New Jersey Transit (NJTR) [16]
• Port Authority Trans-Hudson (PATH) [17]
• Port Authority Transit Corporation (PATCO) [18]
• Southeastern Pennsylvania Transportation Authority (SEPTA) [19]

Defunct major systems

Not all defunct railroads are listed here; most were controlled by a larger railroad.

• Baltimore and Ohio Railroad
• Central Railroad of New Jersey
• Delaware, Lackawanna and Western Railroad
• Erie Railroad
• Lehigh Valley Railroad
• New York Central Railroad
• New York, Ontario and Western Railroad (had trackage rights over NYCRR)
• Pennsylvania Railroad
• Philadelphia and Reading Railroad

Later systems

• Chessie System
• Erie-Lackawanna Railroad
• Penn Central
• Pennsylvania-Reading Seashore Lines

Defunct independent railroads

• Atlantic City and Ocean City Railroad
• Bay Shore Connecting Railroad (jointly owned by CNJ and LVRR)
• Cape May and Sewell's Point Railroad
• Delaware Bay and Cape May Railroad
• Ferro Monte Railroad
• Hibernia Underground Railroad
• Hoboken Manufacturers Railroad
• Langdon Mine Railroad
• Lehigh and Hudson River Railroad
• Lehigh and New England Railroad
• Lehigh and Oxford Railroad
• Manahawken and Long Beach Transportation Company (operated some PRR lines)
• Monmouth Park Railroad
• Mount Hope Tramway
• New York and Long Branch Railroad (jointly owned by CNJ and PRR)
• Normandy Road (owned by U.S. Navy)
• Rahway Valley Railroad
• Raritan River Railroad
• Rockaway River and Montville Railroad
• Rockaway Valley Railroad
• Torrey Railroad
• Tuckerton Railroad
• Union Transportation Company (operated some PRR lines)