The North Jersey Coast Line is mostly the predecessor of the New York and Long Branch Railroad, which was jointly owned by the Pennsylvania and Jersey Central Railroads, that ran joint operations from Perth Amboy to Bay Head. North of Perth Amboy today’s trains use the ex-Pennsylvanian Railroad tracks joining the Northeast Corridor at Rahway before proceeding into New York Penn Station. The line was electrified as far south as Perth Amboy by the Pennsylvania Railroad in 1936. Under New Jersey Transit electrification was extended to Matawan in 1983, with electrification extended to Long Branch where it ends today in 1988. In 2002 the voltage on the line from Matawan to Long Branch was increased from 12.5 kV to 25 kV, therefore today Arrow III cars can only operate on the line on rush hour trains that originate and terminate at South Amboy.

Off-peak and weekends service on the line is hourly service between Long Branch and New York Penn Station. These trains are all push-pull using ALP46 Electric Locomotives pulling Comet IIM, IV, or V single-level coaches or Bombardier Multi-level coaches, with connecting diesel shuttle service running every 2 hours (hourly on Summer weekends) from Long Branch to Bay Head. During rush hours 3 through trains began operating from Bay Head directly into New York Penn Station in 2015, these trains use dual-mode ALP-45DP locomotives. Previously diesel train through service to Bay Head during Rush Hours operated via the Waterfront Connection (that opened in 1991) to and from Hoboken. When through trains to Bay Head began operating in 2015, a few rush-hour electric trains began operating between Long Branch and Hoboken (because their slots into New York-Penn Station were replaced by the Bay Head direct trains). As of the 11/8/2020 schedule, COVID-19 related service cuts have cut all direct North Jersey Coast Line service to Hoboken, although the timetable lists connections at Secaucus Junction (or at Newark-Penn Station for the one remaining AM rush hour Raritan Valley Line train that is currently operating via the Waterfront Connection between Newark-Penn Station and Hoboken) for service to and from Hoboken on rush hour trains.