In 1980, NJ TRANSIT purchased Transport of New Jersey, the State's largest private bus company at that time. Between 1981-85, the services of several other bus companies were incorporated into NJ TRANSIT Bus Operations, Inc. On January 1, 1983, a second subsidiary, NJ TRANSIT Rail Operations, Inc. was launched to assume operations of commuter rail in the State after Congress ordered Consolidated Rail Corporation (Conrail) to cease its passenger operations. A third subsidiary, NJ TRANSIT Mercer, Inc., was established in 1984 when the agency assumed operation of bus service in the Trenton/Mercer County area. In 1992, following a full reorganization, all three subsidiaries were unified and operations were significantly streamlined.

As stakeholders in NJ TRANSIT, State residents are represented by a seven member Board of Directors, appointed by the Governor. Four members are from the general public and three are State officials. The agency is structured to encourage broad public participation in the formation of transit policy for the State. NJ TRANSIT's board meets monthly at NJ TRANSIT headquarters in Newark. The Governor can override board actions by vetoing the board meeting's minutes.

NJ TRANSIT Corporation's Board selects an Executive Director to administer the entire agency. The Executive Director serves as President of all three subsidiaries (NJ TRANSIT Bus Operations, NJ TRANSIT Rail Operations, Inc. and NJ TRANSIT Mercer, Inc.). In addition, NJ TRANSIT employs a Chief Operating Officer to coordinate operations.

Two transit advisory committees provide the agency with additional input from the public. The North Jersey Transit Advisory Committee and the South Jersey Transit Advisory Committee are each comprised of fourteen unsalaried members. Members of the North Jersey Transit Advisory Committee serve four-year terms. Members of the South Jersey Transit Advisory Committee serve three-year terms.