In 1983, NJT assumed operation of all commuter rail service in New Jersey from Conrail, which had been formed in 1976 through the merging of a number of financially troubled railroads.

On December 15, 2003, it opened the Secaucus Junction transfer station, connecting its two commuter networks in northern New Jersey for the first time.

During Hurricane Sandy in October 2012, the rail operations center of NJ Transit was flooded by 8 feet (2.4 m) of water and an emergency generator submerged.

[6] The Governor of New Jersey appoints a thirteen-member Board of Directors, consisting of eleven voting and two non-voting members.

Additional buses are also leased out to several private New Jersey operators, including Coach USA, Lakeland, Transbridge Lines, and Academy.

The project is partnered with the FRA, PANYNJ, NJ Transit and Amtrak, all of which have provided a total funding of $86.5 million.

The extension will better meet the needs of travelers in the area, advance cost-effective transit solutions, improve regional mobility and access, reduce roadway congestion, and attract growth and development.

[11][14][15] As of December 2022, the project is still in its design phase, and NJT was given a $600K federal grant to study transit-oriented development along the proposed extension.

As of 2020, the project is still ongoing after upgrades were made to West Side Avenue Station[11][17] In May 2001, New Jersey acquired the right-of-way of the Lackawanna Cut-Off.

Constructed by the Delaware, Lackawanna and Western Railroad between 1908 and 1911, this provided a direct route with minimal curves and grades between Slateford Junction, two miles (3.25 km) below the Delaware Water Gap, and the crest of the watershed at Lake Hopatcong (Port Morris Junction), the connection with NJT's Montclair-Boonton Line.

All structures, including stations, bridges, interlocking towers and two large viaducts and thousands of fence posts, were made of concrete.

Despite the lack of maintenance on these structures over the past four decades (and in some cases much longer), most are still in operational or near-operational condition.

In 2011, the Lackawanna Cut-Off Restoration Project from Port Morris to Andover, a distance of 7.3 miles (11.7 km), began.

The project was delayed by a lack of environmental permits to clear the roadbed between Lake Lackawanna and Andover.

At the northern terminus, the Walter Rand Transportation Center, paid transfers will be possible to the PATCO Speedline.

The project was originally expected to be completed by 2019,[18] but faced construction delays due to local pushback, lack of funding, and later the COVID-19 pandemic.

Issues regarding the restart of commuter rail service include: With these considerable technical issues, as well as no available space in New York Penn Station for West Shore Line trains, this proposal was put on hold until capacity into New York Penn Station will increase in the future.

The leadership of the municipalities along the route have been organizing for decades to get service running again[32][33] and have been rezoning the areas around the former train stations ever since being told by NJ Transit that the number of projected riders is too low to justify investment.

[34] The Monmouth-Ocean-Middlesex (MOM)[35][36] line is a proposed south and central New Jersey commuter rail route to New Brunswick, Newark and New York's Penn Station.

This would restore service previously provided by the Central Railroad of New Jersey with similar station sequences.

It would run on a 40.1-mile rail corridor and would provide diesel commuter rail service from Monmouth Junction (South Brunswick), where the Jamesburg Branch partially joins the Northeast Corridor (NEC), south to Lakehurst in the interior of northern Ocean County.

It would proceed southward from Farmingdale to Lakehurst, passing through Howell, Lakewood, Jackson, Toms River, Townships, and Lakehurst/Manchester.

In mid-February 2008, New Jersey Governor Jon Corzine withdrew the Monmouth Junction alignment from the MOM Plan.

Corzine opted to endorse the two remaining alternate alignments (via Red Bank or Matawan-Freehold, the latter which is currently part of the Henry Hudson Rail Trail).

NJT referred to the project as Access to the Region's Core, which would have used dual-power locomotives and a new rail junction at Secaucus, allowing for a one-train ride between the Port Jervis, Main, Bergen County, Pascack Valley, and Raritan Valley lines and New York Penn Station.

[47] Both the Federal Transit Administration and the Port Authority made public commitments of $3 billion to the project.