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New York City Subway station in Brooklyn

As part of negotiations between New York City and 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.

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, Bay Ridge Avenue's platforms would have been lengthened from to Progress on the extensions did not occur 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 (633000.0 in 1925 is equivalent to about <calculated amount> in recent years). The BMT had been ordered by the Transit Commission to lengthen these platforms since September 1923. The NYCBOT received bids for the project on February 25, 1926. The contract was awarded to the Corson Construction Company for $345,021 (345021.0 in 1926 is equivalent to about <calculated amount> in recent years). 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 Bay Ridge Avenue, to the W. M. Walsh Corporation for $6,585 in preparation of the construction of platform extensions (6585.0 in 1967 is equivalent to about <calculated amount> in recent years). 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. As part of the renovation project, the station's platforms were extended at its northern and southern ends, for a total of , and the station's elaborate mosaic tile walls were covered over with white cinderblock tiles. The latter change, which was also made to 15 other stations on the BMT Broadway and Fourth Avenue Line, was criticized for being dehumanizing. The NYCTA spokesman stated that the old tiles were in poor condition and that the change was made to improve the appearance of stations and provide uniformity. Furthermore, it did not consider the old mosaics to have "any great artistic merit".

As part of the Metropolitan Transportation Authority's 2015–2019 Capital Program, the station, along with thirty other New York City Subway stations, were scheduled to undergo a complete overhaul as part of the Enhanced Station Initiative. Updates were to include cellular service, Wi Fi, USB charging stations, interactive service advisories and maps, improved signage, and improved station lighting. From January to May 2016, Grimshaw Architects worked on a design for the station's renovation, with Arup Group acting as a consultant. The award for Package 1 of the renovations, which covered renovations at the Prospect Avenue, 53rd Street, and Bay Ridge Avenue stations on the BMT Fourth Avenue Line, was awarded on November 30, 2016. Citnalta Forte Joint Venture was selected to renovate the three stations under a $72 million design–build contract, the first such contract in the subway system's history. The station closed on April 29, 2017 for these renovations and reopened on October 13, 2017.