Located at the intersection of 116th Street and Lenox Avenue in Harlem, it is served by the 2 and 3 trains at all times.

The 116th 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 platforms contain exits to Lenox Avenue's intersection with 116th Street and are not connected to each other within fare control.

[3]: 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.

[3]: 148  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,[5] in which it would construct the subway and maintain a 50-year operating lease from the opening of the line.

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

[3]: 182 The 116th Street station was constructed as part of the IRT's East Side Branch (now the Lenox Avenue Line).

[5][6]: 252  The excavation was relatively easy because the subway was under one side of Lenox Avenue and there were no street railway tracks to work around.

[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.

[18] The New York City Transit Authority (NYCTA) announced plans in 1956 to add fluorescent lights above the edges of the station's platforms.

This was done to correct a major water problem that had existed for many years due to the presence of the Harlem Creek and other underground streams, which caused extensive flooding, water damage, and seepage problems that occasionally contributed to severe service disruptions.

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