Senator Frank Lautenberg, who died in 2013, was a transit advocate who had worked to allocate federal funds for the project.

NJ Transit's rail operations are split between two divisions, a legacy of their roots in separate railroads.

While the opening of the Kearny Connection and Waterfront Connection in 1996 allowed for the implementation of some interdivisional trains, including the "Midtown Direct" service to New York Penn Station on the Hoboken Division's Morris & Essex Lines, direct passenger transfers between the divisions were still not possible.

[10][11] On June 1, 2009, Edison Parkfast, a private company, opened the first parking lot near the station,[12] with space for 1,094 cars.

[15][16] In anticipation of increased ridership for Super Bowl XLVIII in February 2014, NJT extended the lower-level platforms at Secaucus Junction by 120 ft (37 m) to accommodate multi-level 10-car train sets which could handle about 1,400 to 1,800 passengers per trip.

[18] On February 2, 2014, a limited number of Amtrak trains made stops at Secaucus for passengers going to Super Bowl XLVIII.

[19] Local officials have indicated a desire to have regular Amtrak service stop at Secaucus Junction after American Dream Meadowlands opened in October 2019,[20] however, as of 2024, this has not been implemented.

[21] In 2021 NJ Transit authorized studies for alternative options between the Meadowlands Sports Complex and Secaucus Junction including a bus "transitway".

[22][23][24] Further funding for design was approved in 2023 for an exclusive bus transitway planned to go into service for the 2026 FIFA World Cup.

The plan would alleviate pressure on the NJ Transit/Amtrak route under the Hudson, after the cancellation of the Access to the Region's Core tunnel project by New Jersey Governor Chris Christie in October 2010.