The 79th 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.

The remaining portion of the original station interior is a New York City designated landmark and listed on the National Register of Historic Places.

[7]: 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.

[7]: 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,[8] under which it would construct the subway and maintain a 50-year operating lease from the opening of the line.

[3][7]: 186  The opening of the first subway line, and particularly the 79th Street station, helped contribute to the development of the Upper West Side.

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

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

[13]: 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.

[27][24] In November 1959, the Warshaw Construction Company received a contract to remove fifteen entrance/exit kiosks on IRT lines, including two at the 79th Street station.

[28] On June 28, 1964, the New York City Transit Authority (NYCTA) awarded a contract to construct additional entrances at the station to Delma Engineering Corporation for $212,874 (equivalent to $2,091,281 in 2023).

Additional columns between the tracks, spaced every 5 feet (1.5 m), support the jack-arched concrete station roofs.

[5]: 3–4 The remainders of both platforms have cream-colored tiles and a salmon trim line with "79TH ST" written on it in black Sans Serif font at regular intervals.

[47][48] The southbound platform is fully staffed, containing a turnstile bank, token booth, staircase going up to the northwest corner of West 79th Street and Broadway, and passageway separated from the platform by a steel fence leading to a staircase that goes up to the southwest corner of the intersection.

This passageway has a High Entry-Exit Turnstile to the platform, with walls made of cinder block tiles.

[5]: 4–5, 17 [49] The northbound platform's fare control is unstaffed, containing a turnstile bank, now-closed customer assistance booth, staircase going up to the southeast corner of West 79th Street and Broadway, and passageway separated from the platform by a steel fence leading to a staircase that goes up to the northeast corner of the intersection.

[5]: 4–5, 17 [49] The street staircases on both sides contain relatively simple, modern steel railings like those seen at most New York City Subway stations.