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New York City Subway station in Brooklyn

As part of negotiations between New York City, the Brooklyn Rapid Transit Company (BRT), and the Interborough Rapid Transit Company for the expansion of the city's transit network, the line was leased to a subsidiary of the BRT. The agreement, known as Contract 4 of the Dual Contracts, was signed on March 19, 1913. The station's opening was marked with a competition between two trains heading from Chambers Street station in Manhattan to the Coney Island station, one heading via the West End Line and the other via the Sea Beach Line; the latter got to Coney Island first.

On June 27, 1922, the New York State Transit Commission commissioned its engineers to examine platform lengthening plans for 23 stations on the lines of the Brooklyn–Manhattan Transit Corporation (BMT), the successor to the BRT, to accommodate eight car trains. As part of the project, 59th Street's platforms would have been lengthened from to Though the Transit Commission ordered the BMT to lengthen these platforms in September 1923, no further progress was made until February 16, 1925, when the New York City Board of Transportation (NYCBOT) commissioned its engineers to examine platform lengthening plans for this and eleven other stations along the Fourth Avenue Line. It estimated the project would cost $633,000 The NYCBOT received bids for the project on February 25, 1926. The contract was awarded to the Corson Construction Company for $345,021 The extensions opened on August 1, 1927. The city government took over the BMT's operations on June 1, 1940. In the 1960s, the New York City Transit Authority (NYCTA) started a project to lengthen station platforms on its lines in Southern Brooklyn to to accommodate 10 car trains. On July 14, 1967, the NYCTA awarded a contract to conduct test borings at eleven stations on the Fourth Avenue Line, including 59th Street, to the W. M. Walsh Corporation for $6,585 in preparation of the construction of platform extensions. The NYCTA issued an invitation for bids on the project to extend the platforms at stations along the Fourth Avenue Line between 45th Street station and Bay Ridge–95th Street, including this station, on May 3, 1968. However, work had already started on the platform extension project in February. The platforms were extended by to the north. In 1983, the MTA added funding for a renovation of the 59th Street station to its 1980–1984 capital plan. Elevator access for this station had been proposed for the late 2010s. However, the installation of elevators was delayed due to a column replacement project above this section of the Fourth Avenue Line. Both the column replacement and the elevator installation required temporary lane closures on Fourth Avenue, a major artery. An elevator contract was supposed to be awarded in November 2016, but was pushed back to July 2018. A $55.2 million contract for the installation of three elevators at the 59th Street station was awarded in late 2018. Substantial completion was expected in July 2020, but the project was delayed and the elevators opened on November 6, 2020. The final component of the project was completed in June 2021.

The street level entrances are at the southern end of the station, with one entrance along either side of Fourth Avenue between 60th and 61st Streets. This part time exit is unstaffed and has High Entry Exit Turnstiles. There are also four exits to Fourth Avenue and 59th Street, which includes two staircases to the northeast corner, along with one staircase and elevator to the northwest corner, at the north end of the station. Each entrance has its own small mezzanine, and allows for crossovers between platforms.

Immediately south of the station, there are tunnel stub headings running straight from the local tracks. They run for about 150 feet (46 m) and would have been for a line to Staten Island via the Staten Island Tunnel under the Narrows, which was aborted by Mayor Hylan before it was completed. There is a "maintenance of way" shed that was built on the southbound trackway. The northbound trackway is unobstructed, albeit much darker. The northbound trackway ends on a brick wall, with evidence of a void space beyond. South of this station, the bridge over the LIRR Bay Ridge Branch has four trackways, with the outer tracks occupying the two western ones. The tracks of the BMT Fourth Avenue Line are under the western half of Fourth Avenue at this point so that two additional tracks could be laid in the future if traffic warranted it. The original proposal planned a connection from a point between 65th and 67th Streets, just south of the station, running to Arrietta Street near the Tompkinsville station in Tompkinsville, Staten Island. A later plan called for a connection to St. George, Staten Island, near St. George Terminal. Construction for the latter started in 1923, but the project was canceled in 1925.

The Basilica of Our Lady of Perpetual Help, the largest church in Brooklyn, is located one block east on Fifth Avenue between 59th and 60th Streets. The Brooklyn Army Terminal is located two blocks west, along with the NYC Ferry pier there, though there is no free transfer between the subway and the ferry.