In the New York City area, it ranks only behind Pennsylvania Station, Grand Central Terminal, and Secaucus Junction, with over 1,000 trains passing through it every day, while there is a direct rail connection to John F. Kennedy International Airport via AirTrain JFK. There are also elevator connections to the Archer Avenue Line of the New York City Subway at Sutphin Boulevard – Archer Avenue (E J Z trains), directly below. The area just outside is served by several local bus routes, with more available within a few blocks of the station.

All LIRR services except the Port Washington Branch pass through Jamaica Station. The Main Line westwards leads to Long Island City, Queens and Pennsylvania Station in Manhattan, while the Atlantic Branch diverges along Atlantic Avenue to Atlantic Terminal in Brooklyn. The Montauk Branch also serves one daily trip to Long Island City. East of Jamaica, these three lines diverge, with some branch services using the Main Line, some using the Atlantic Branch, and some using the Montauk Branch.