[8] The IRT's 45th Road–Court House Square station opened on November 5, 1916, as part of a two-stop extension of the line from Hunters Point Avenue to Queensboro Plaza.

[19][20]: L6 In the late 1920s and early 1930s, the city-owned Independent Subway System (IND) constructed the first sections of the Crosstown and Queens Boulevard Lines.

[22][27][28][29] This was in spite of protests from local civic and industry leaders, due to the numerous factories in the surrounding area.

[39]: 9 [40][41][42] Two of these buildings, Citigroup Center and 399 Park Avenue, were located near the Lexington Avenue–53rd Street station, the next stop southbound on the Queens Boulevard Line.

The company selected the Court Square site due to its proximity to the Queens Boulevard subway.

[42] In 2000, the MTA began designing a second in-system passageway between the Flushing and Crosstown Line stations.

To compensate Crosstown riders going into Queens, a free out-of-system transfer to the Flushing Line station was created.

[46][47] In addition, moving walkways in the corridor between the Crosstown and Queens Boulevard Line platforms were installed in December 2001.

[46][47][48] The moving walkway was subsequently found to have limited benefits: it saved commuters an average of 9 seconds; was often out of service; and could only operate in one direction toward the Queens Boulevard Line platforms.

[49][50] In October 2005, Citigroup announced they would be funding the passageway between the Flushing and Crosstown line stations, as a zoning requirement for the construction of the Court Square Two building.

[68][69] In December 2019, the MTA announced that the Queens Boulevard Line platforms would become ADA-accessible as part of the agency's 2020–2024 Capital Program.

[72][73] A future developer will construct an elevator from the westbound Queens Boulevard Line platform to the mezzanine.

[74] The MTA began receiving bids for the construction of a ramp to the eastbound platform in May 2023,[75] and the contract was awarded that December.

The main fare control area has a ceiling with a skylight, as well as a turnstile bank, token booth, and two staircases.

One has two escalators and goes up to south side of 44th Drive inside a Citibank location next to the tower, and the other is open weekdays only and leads to the entrance plaza of One Court Square.

[47] Lining the walls of this passageway is Stream, a glass mosaic mural by Elizabeth Murray, which was installed in 2001.

[87]: 2985  They are composed of numerous panels of composite fiberglass resin, lighter than conventional concrete and designed to resist corrosion and thermal expansion.

[57][58] Both platforms have beige windscreens that run along their entire lengths and brown canopies with green frames and support columns except for a small section at their north ends.

A single staircase from each platform goes down to a combined waiting area and crossunder, where a turnstile bank provides entrance and exit from the station.

[20]: K2  Two escalators and a staircase, located within an enclosed structure, lead directly to the complex's underground mezzanine area via a new transfer passageway.

[57][78] The northbound platform's elevator also leads to the underground mezzanine within fare control, stopping at the station house level but bypassing the street along the way.

[27][28] The platform walls have a scarlet lake trim line with a dark olive border and mosaic name tablets reading "23RD ST. – ELY AVE." in white sans serif letting on a dark olive background and scarlet lake border.

[92] Below the trim line are small tile captions alternating between "23RD" and "ELY" in white on black, and directional signs in the same style are present below some of the name tablets.

[96][97] Red I-beam columns run along both platforms at regular intervals with alternating ones having the standard black station name plate in white lettering.

[100] The entrance was renovated and the elevator was added as part of the construction of the Skyline Tower at the northeast corner of this intersection.

[78][26] The long passageway to the IND Crosstown Line platform extends to the south, past the crossover.

[46][78] Prior to the construction of the passageway, this exit contained a full-time token booth and staircases to both sides of 44th Drive.

This section of the tracks are not used in regular service, though until April 19, 2010, trains traveled over this connection to continue to Forest Hills–71st Avenue at various times of the day.

[78] The site of the 5 Pointz building at Jackson Avenue and Davis Street,[78] which was famously covered in graffiti until its demolition in 2014,[107] is visible just south of the Flushing Line station and can be seen by passing 7 and <7>​ trains.

[109] Trader Joe's eventually opened immediately adjacent to the Station and the Court Square Diner.