The 66th Street station was constructed for the Interborough Rapid Transit Company (IRT) as part of the city's first subway line, which was approved in 1900.

[5]: 21  However, development of what would become the city's first subway line did not start until 1894, when the New York State Legislature passed the Rapid Transit Act.

It called for a subway line from New York City Hall in lower Manhattan to the Upper West Side, where two branches would lead north into the Bronx.

[5]: 161 The Rapid Transit Construction Company, organized by John B. McDonald and funded by August Belmont Jr., signed the initial Contract 1 with the Rapid Transit Commission in February 1900,[7] under which it would construct the subway and maintain a 50-year operating lease from the opening of the line.

[6]: 4  Belmont incorporated the Interborough Rapid Transit Company (IRT) in April 1902 to operate the subway.

East Side local trains ran from City Hall to Lenox Avenue (145th Street).

[10] To address overcrowding, in 1909, the New York Public Service Commission proposed lengthening the platforms at stations along the original IRT subway.

[11]: 168  As part of a modification to the IRT's construction contracts made on January 18, 1910, the company was to lengthen station platforms to accommodate ten-car express and six-car local trains.

The original subway north of Times Square thus became part of the Broadway–Seventh Avenue Line, and all local trains were sent to South Ferry.

[26][22] On November 29, 1962, a new entrance at the station opened, leading to the lobby of the Philharmonic (now David Geffen) Hall of Lincoln Center.

This entrance was built as part of a $10.2 million underground complex by the New York City Parks Department for the Philharmonic Hall.

[28] In 1981, the MTA announced the creation of its Culture Stations program to install public art in the subway.

The Culture Stations program was started to deter graffiti, and was inspired by legislation in the New York City Council that mandated that 1% of the cost of constructing public buildings be used for art.

[31] The MTA announced in 1983 that it would allocate funding to renovate the 66th Street station as part of its capital program.

[36] According to New York City Planning Commission chairwoman Sylvia Deutsch, the MTA had chosen to delay the 66th Street project.

[46] At the time of the renovation, the station had seen a 12 percent increase in ridership over the past few years because of the presence of new apartment buildings and popular businesses nearby.

[48] The 66th Street station received esthetic improvements in early 2024 as part of the MTA's Re-New-Vation program.

[56]: 37  As part of the station's 1990s renovation, plaques with the initials "L" and "C", with the number "66" overlaid on them, were installed; they are designed in a style similar to the original mosaics.

[59][60] The artwork, installed in 2001, consists of 22 panels that depict a diva in various settings, a reference to the station's location next to Lincoln Center.

A third set of exits, at the extreme south end of the southbound platform, contains a stair to the southwestern corner of Columbus Avenue and 65th Street, as well as a passageway to David Geffen Hall.

[61] The station provides access to Lincoln Center for the Performing Arts just to the south, with Alice Tully Hall just to the west.