The line was constructed in two main portions by the Interborough Rapid Transit Company (IRT), a private operator.

The original subway turned west across 42nd Street at the Grand Central station, then went north at Broadway, serving the present-day IRT Broadway–Seventh Avenue Line.

The second portion of the line, north of 42nd Street, was constructed as part of the Dual Contracts, which were signed between the IRT; the Brooklyn Rapid Transit Company, via a subsidiary; and the City of New York.

[4][5] Finally, South Ferry is within walking distance of Bowling Green, and is right next to the corresponding station on the Broadway–Seventh Avenue line.

The IRT submitted an offer for what became its portion of the Dual Contracts on February 27, 1912,[23] and construction was soon halted on Section 6.

[10] In 1928, the New York City Board of Transportation proposed to extend platforms at all stations between Brooklyn Bridge and Grand Central, except for 33rd Street.

In 1957, the New York City Transit Authority started work on a $138 million modernization program for the Lexington Avenue Line to improve and speed up service.

[33] Work on the reconstruction of the Brooklyn Bridge station started on May 18, 1959, and continued without interruption until it was completed on September 1, 1962.

At the center of the enlarged platforms, a new overhead passage was built, providing more direct access to the Municipal Building.

[34][33] On July 23, 1959, the Board of Estimate approved the contract for the construction of express platforms at Lexington Avenue–59th Street.

The project cost $6.5 million and was completed three months prior than originally planned when the new platforms opened on November 15, 1962.

[40] Because the Lexington Avenue Line during the 1970s was known to frequent muggers due to the dilapidated state of the subway at the time, the Guardian Angels, founded by Curtis Sliwa, began operations on February 13, 1979, by conducting unarmed night patrols on the 4 train in an effort to discourage crime.

[43][44] As a result of the crash, new safety protocols were put in place and there was a partial implementation of automation of the New York City Subway.

[45] The Metropolitan Transportation Authority announced in 2024 that it would begin installing 5G cellular equipment on the Lexington Avenue Line north of the Grand Central–42nd Street station in mid-2025.

With the city's economic and budgetary recovery in the 1990s, there was a revival of efforts to complete construction of the Second Avenue Subway.

[54] Once fully built, the line will run from 125th Street and Lexington Avenue to Hanover Square in the Financial District.

[56] East Side Access, completed in 2023, brought Long Island Rail Road service into Grand Central.

[57]: 7 Crowding on the line is so bad that riders are routinely stranded on the platform, having to wait for multiple trains to pass before being able to board.

[59] In June and July 2017, The New York Times found that during an average weekday, 10% to 15% of the trains scheduled to run through Grand Central–42nd Street were canceled.

The MTA mandated that the developers pay for station improvements at Grand Central to allow for the building's construction.

[61] In 2015, SL Green, the developer, gave $220 million toward the building's construction,[62] of which two-thirds of the money would be used for station redesign;[63] this marked the largest private investment to date to the New York City Subway system.

[64] The new building would also coincide with the MTA's East Side Access project, and station improvements due to One Vanderbilt's construction would provide extra capacity for over 65,000 new passengers going into the New York City Subway at Grand Central–42nd Street.

[65][66] The improvements include an underground connection between Grand Central Terminal and One Vanderbilt; new mezzanines and exits for the subway station; and three new stairways to each of the Lexington Avenue Line platforms.