It is the third-busiest rail hub in the New York area, behind Penn Station and Grand Central Terminal.

Over 1,000 trains pass through each day, the fourth-most in the New York area behind Penn Station, Grand Central Terminal, and Secaucus Junction.

The Jamaica station is located on an embankment above street level and contains six platforms and ten tracks for LIRR trains.

Due to this, all LIRR passenger service barring the Port Washington Branch operates through here, with it being common for commuters to "Change at Jamaica" between trains to travel between points on Long Island and the four New York City terminals.

Starting in or about 2028, the Jamaica station will also serve trains on the Long Island extension of Amtrak's Northeast Regional intercity rail service.

The other station known as Jamaica–Beaver Street was built by the South Side Railroad of Long Island on the Atlantic Branch.

When the LIRR acquired the SSRRLI in 1867, the depot was moved to the south side of Beaver Street crossing on a stub track.

Low platforms for this station stop were located on the north side of Beaver Street crossing.

Originally the site of the "SJ Tower," which was used to keep trolleys and trains from colliding with one another until the grade crossing was eliminated in 1913, it was built on November 15, 1917.

[13] In September 1983, the LIRR announced that De Leuw, Cather & Company would complete a conceptual design for the construction of express bypass tracks through the station.

[15][16] The plan would have rebuilt six miles of tracks on the Main Line between the Van Wyck Expressway and Bellerose, and construct a new southern platform.

The first phase, which was slated to begin in 1988 and be completed by 1994 and would cost $192.5 million, would construct a new master control tower and a rider overpass, and install new signals and switches.

The second phase, which would cost $150 million, would move platforms to provide space for the construction of westbound and eastbound express tracks through the station and build some elevated trackage.

[20] On September 11, 1989, the LIRR announced that it had dropped most of its planned reconstruction of Jamaica due to changes in commuting patterns and technology.

It was carried out in conjunction with the construction of AirTrain JFK's terminal (the Port Authority of New York and New Jersey contributed $100 million toward the project).

[22] The focal point of the project was the Jamaica Control Center, built by Tishman Construction Corporation and Bechtel.

[23] Overall, the renovations enlarged the station and have made it more modern and efficient, providing easier access to all eight LIRR tracks.

The entire station complex, including AirTrain and the subway, is compliant with the Americans with Disabilities Act of 1990 (ADA).

[24] As part of a series of LIRR readiness projects in preparation for the East Side Access extension to Grand Central Terminal, the MTA had adjusted track layouts at Jamaica station to straighten train paths and install high-speed switches.

[26] The completion date was later pushed back to July 2019,[30] but as of March 2019[update], is planned to be finished in 2021 at a cost of $380 million.

In January 2025, it was officially announced that a new Long Island branch of Amtrak's Northeast Regional would be created, running east from Penn Station and points south & west to Ronkonkoma via the LIRR's Main Line, with intermediate stops at Jamaica and Hicksville.

[36] The main entrance to the station, where tickets may be purchased and where waiting areas are located, is a 100-year-old building that also serves as the offices and headquarters of the Long Island Rail Road Company.

It is accessed by escalator or elevator from street level as well as via an enclosed bridge connecting it to the LIRR station.

West of the station the track curves to the left and runs south, above the Van Wyck Expressway.