[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.

[4]: 3  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.

On January 24, 1901, the Board adopted a route that would extend the subway from City Hall to the Long Island Rail Road (LIRR)'s Flatbush Avenue terminal station (now known as Atlantic Terminal) in Brooklyn, via the Joralemon Street Tunnel under the East River.

[6]: 83–84 [7]: 260–261  Contract 2, which gave the IRT a 35-year lease,was executed between the commission and the Rapid Transit Construction Company on September 11, 1902.

Belmont submitted a revised proposal to the Rapid Transit Commission in April 1905 to widen the line to four tracks.

[11][12] An extension to Atlantic Avenue, including a station at Hoyt Street, opened on May 1, 1908, completing the Contract 2 IRT line.

[17] The Broadway–Seventh Avenue Line would split into two branches south of Chambers Street, one of which would turn eastward through Lower Manhattan, run under the East River via a new Clark Street Tunnel, and connect with the existing Contract 2 IRT Brooklyn Line at Borough Hall.

[28][29] In November 1946, the New York City Board of Transportation awarded a $733,200 contract for the lengthening of the Hoyt Street station's platforms.

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

[34] In 1982, the Urban Mass Transportation Administration gave a $66 million grant to the New York City Transit Authority.

The full-time fare control is at the west end of the station, and contains one token booth and a turnstile bank for each platform.

[41] The northbound platform's part-time fare control area also had an exit-only stair to the northwest corner of Duffield and Fulton Streets, but it was closed due to security concerns.