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 original section of the station 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.

[6]: 3  A plan was formally adopted in 1897,[7]: 148  and all legal conflicts concerning the route alignment were resolved near the end of 1899.

[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.

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

[3][7]: 186  The opening of the first subway line, and particularly the 116th Street station, helped contribute to the development of Morningside Heights and Harlem.

[5]: 8 After the first subway line was completed in 1908,[14] the station was served by West Side local and express trains.

Express trains began at South Ferry in Manhattan or Atlantic Avenue in Brooklyn, and ended at 242nd Street in the Bronx.

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

[17]: 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.

[20] A contract for the platform extensions at 116th Street and eight other stations on the line was awarded to Spencer, White & Prentis Inc. in October 1946,[25] with an estimated cost of $3.891 million.

[30] The university brought up the issue again at a meeting of the New York City Board of Estimate in 1963,[31] after a student was killed while crossing the street.

Sixty-eight hundred students and faculty members signed a petition to remove the kiosk in February 1964.

In 1965, Columbia University and Barnard College had announced that they would each spend $5,000 (equivalent to $48,342 in 2023) to decorate the new entrances to fit in with their campuses.

[41] When skip-stop service began on August 21, 1989, it was only implemented north of 137th Street–City College on weekdays, and 116th Street was served by both the 1 and the 9.

[50] As a condition of the funding allocation for the station renovation, the university wanted work on the project to be expedited.

Residents of Morningside Heights approved of the renovation plans, but were concerned that the expedited repairs would come at the cost of damaging the stations' historic elements.

The MTA was expected to decide whether preservation or speed would be prioritized in the station renovation projects by the end of 2002.

[50][51] The MTA had planned to install a small bronze subway track and train to be inlaid within the station walls surrounded by sepia-toned photographs of the neighborhood at 116th Street.

In December 2002, Manhattan Community Board 7 voted in favor of the plan to include artwork from the MTA's Arts for Transit program at the 103rd Street station, which was not landmarked.

[59][60] The artwork, installed in 1991 as part of the MTA Arts for Transit program, was originally intended to be temporary.

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

[5]: 3  There is also an exit-only staircase near the southern end of the northbound platform that leads to the east side of Broadway at 115th Street, outside the Alfred Lerner Hall.

At the corners of the station house were limestone quoins, which supported a copper-and-terracotta gable roof facing west and east.

The doorways were centrally located on the north and south walls of the control house, topped by terracotta finials and a rounded gable.