This is one of the deepest stations in the subway system, requiring several banks of long escalators or elevators.

Originally, the station was intended to be a transfer point for Sixth Avenue/Queens Boulevard and Broadway/Second Avenue services.

The unopened entrance at Third Avenue was fitted with multiple elevators, and the station's false ceiling was removed.

The Second System was a plan to expand the city-owned and -operated Independent Subway System (IND), which often ran in direct competition with the two privately owned subway companies in the city, Interborough Rapid Transit (IRT) and Brooklyn-Manhattan Transit Corporation (BMT).

The IND line was to be built on the upper portion of the bi-level 63rd Street Tunnel, which would run under the East River.

[11]: 5, 21  Directly to the west of the station is a crossover to facilitate a connection between the BMT and IND lines.

As early as 1976, the Program for Action had been reduced to seven stations on the Archer Avenue and 63rd Street lines and was not projected to be complete for another decade.

[26] East of this station on the IND side are turnouts heading southwest for a connection to Phase 3 of the Second Avenue Subway, clearly visible from a moving train, which would allow future service from Queens towards Midtown and Downtown Manhattan.

The two tracks on the lower level of that tunnel are being connected to the Long Island Rail Road (LIRR) via the East Side Access project.

[15] The project brings trains from the LIRR's Main Line to Grand Central Terminal.

[29] East of this station on the BMT side, the planned track connections to the Second Avenue Subway curved slightly north.

[31] As part of the project, the station was to undergo renovation to finish the BMT side, which would serve Second Avenue Line trains.

[39] In spring 2012, temporary blue walls separating most of the IND and BMT sides were erected for the duration of construction.

Passengers travel between the new mezzanine and the platforms using four high-speed elevators, similar to the layout of several other deep-level stations.

[2][8]: 33 On July 22, 2001, concurrent with the closure of the IND Sixth Avenue Line tracks of the Manhattan Bridge, B and Q train service to this station ceased and was replaced with a full-time shuttle.

[58]: 5 [59]: 2 [60][61][62] When this happened, a free MetroCard out-of-system transfer to the Lexington Avenue–59th Street station was added.

[48] As with other stations constructed as part of the Program for Action, the Lexington Avenue–63rd Street station contained technologically advanced features such as air-cooling, noise insulation, CCTV monitors, public announcement systems, electronic platform signage, and escalator and elevator entrances.

[32] An eastern mezzanine at Third Avenue, along with stairwells to the platforms, was partially completed in the 1980s but not opened along with the rest of the station.

A shaftway, identical to the one on the Lexington Avenue side, contained a single stairway, as well as beams that may have been intended to support escalators.

[76] On each platform level, both waiting areas have a piece of the Jean Shin artwork "Elevated.

During the Second Avenue Subway renovations, Jean Shin created an artwork called Elevated as part of the MTA Arts & Design program.

On the south east-corner entrance at Third Avenue, there are ceramic tiles depicting construction beams and the cranes that dismantled the el.

The platform level features semi-transparent and reflective glass depicting vintage scenes of the neighborhood.

[84] In 2017[update], Lexington Avenue–63rd Street recorded 6,389,408 entries, making it the 70th busiest station in the 425-station system.