The station initially had eight tracks to allow BMT and IRT passengers to transfer between the Astoria, Flushing, and Second Avenue elevated lines.

The New York Public Service Commission adopted plans for what was known as the Broadway–Lexington Avenue route (later the Broadway Line) in Manhattan on December 31, 1907.

In Queens, which heretofore had no subway service, two lines had been proposed, both extending from an interchange station (later Queensboro Plaza) in Long Island City.

As part of the Dual Contracts, the IRT was given ownership of both lines, but the BRT was given trackage rights over the routes, allowing both companies to share revenue from their Queens operations.

The IRT had direct service into Manhattan via the Steinway Tunnel, as well as via the Queensboro Bridge to the Second Avenue elevated line.

However, BRT trains from the 60th Street Tunnel and the Broadway Line in Manhattan could not run north or east of Queensboro Plaza, as they were wider.

[18][19] The service on the Flushing and Astoria lines east of Queensboro Plaza was shared by the IRT and BMT until 1949.

[22] On October 17, 1949, the $1.375 million renovation of the station was completed which allowed the rerouting of trains between Manhattan and Queens.

[23] Much of the mezzanine was rebuilt as part of the project, including the pedestrian bridges leading to either side of Queens Plaza.

[26] the New York City Board of Transportation announced that platforms on the Flushing Line would be lengthened to 11 IRT car lengths.

With the exception of the Queensboro Plaza station, which was already 600 feet (180 m) long, the platforms were only able to fit nine 51-foot-long IRT cars beforehand.

[23] As part of the project, an overpass was constructed from the station towards Queens Plaza North, spanning the site of the demolished platforms.

The project would have also included a new bus terminal, access to a parking garage, and a pedestrian mall on the north side of Northern Boulevard.

[46] The R train's northern terminal was swapped with that of the N in 1987, so the N went to Ditmars Boulevard (serving Queensboro Plaza) and the R went to 71st Avenue.

[47] In April 1993, the New York State Legislature agreed to give the MTA $9.6 billion for capital improvements.

Some of the funds would be used to renovate nearly one hundred New York City Subway stations,[48][49] including Queensboro Plaza.

[53][54] In 2018, it was announced that the Queensboro Plaza station may receive elevators as part of a process to expand the New York City Subway system's accessibility.

[56] Accessibility improvements at Queensboro Plaza were approved in December 2021,[57][58] and the MTA began preliminary work shortly afterward.

[65][66] In February 2022, developer Grubb Properties filed plans for a 26-story apartment tower at 25–01 Queens Plaza North.

A computer assisted tower was installed on the south end, as part of the IRT Flushing Line automation.

The north side was used by Astoria trains, but instead of going through the 60th Street Tunnel, they went over the Queensboro Bridge to the elevated IRT Second Avenue Line.

Since the platforms were IRT-size, the BMT used its own elevated cars to provide service on the lines, with a required transfer at Queensboro Plaza.

[35] The station's only exits are through a mezzanine located below the lower level (and formerly connected to the now torn-down BMT platforms to the west).

The protagonist astronaut ("Brent") unknowingly enters the ruins of an underground station; upon seeing the words "Queensboro Plaza" in tiles, and finding an advertisement for the New York Summer Festival, he realizes that he is indeed on Earth and not another planet, and that New York City has been destroyed in a nuclear war.

The station and nearby MetLife Plaza were a regular CG composite as location shots between scenes in ABC series Ugly Betty.