The buses on Staten Island had been operated by a private company operating under a franchise that expired in 1946. The IRT and BMT systems were acquired by the city on June 1, 1940, for $317,000,000 and consolidated with the IND into the New York City Board of Transportation (NYCBOT). The third, the public Independent Subway System (IND) was owned and operated by the City of New York. Two of them were built and operated by private companies: August Belmont's Interborough Rapid Transit Company (IRT) and the Brooklyn–Manhattan Transit Corporation (BMT). The subway system today is composed of what once were three separate systems in competition with one another. Sarah Feinberg and Craig Cipriano served as interim presidents until May 2, 2022, when Richard Davey was hired to assume the role on a permanent basis. The position of president was vacant as of February 21, 2020, following the resignation of its most recent president, Andy Byford. The Transit Authority has its own management structure which is responsible for its day-to-day operations, with executive personnel reporting to the agency president. The executive director of the MTA is, ex officio, executive director of the Transit Authority. The chairman and members of the MTA, by statute, also serve as the chairman and members of the Transit Authority, and serve as the directors of the Manhattan and Bronx Surface Transit Operating Authority. The Authority is also sometimes referred to as NYCT (for New York City Transit), or simply the TA (for Transit Authority).

Newer contracts and RFPs, however, have also used the popular name.

The New York City Transit Authority is now known popularly as MTA New York City Transit (NYCT), (or more specifically on the vehicles, MTA New York City Bus and MTA New York City Subway), though the former remains its legal name for documents and contracts. As part of establishing a common corporate identity, the Metropolitan Transportation Authority in 1994 assigned popular names to each of its subsidiaries and affiliates.

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