The plan for the line was initially adopted on June 1, 1905, before being approved by the Appellate Division of the Supreme Court of New York on June 18, 1906, after the Rapid Transit Commission was unable to get the necessary consents of property owners along the planned route.

[3][9] The station was the original terminal for the line[10] until a one-stop southward extension to Bay Ridge–95th Street opened on October 25, 1925.

[11] 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.

[12][13] 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.

[18][19] In the 1960s, the New York City Transit Authority (NYCTA) started a project to lengthen station platforms on its lines in Southern Brooklyn to 615 feet (187 m) to accommodate 10-car trains.

[20] 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 (equivalent to $60,172 in 2023) in preparation of the construction of platform extensions (equivalent to $60,172 in 2023).

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 renovation repaired staircases, rebuilt the station's ventilation, and installed new tiling for walls and floors as well as ADA-compliant yellow safety treads along the platform edges.

The modern renovation restored these tiles, and added an Arts for Transit glass mosaic inspired by the old homes of the Bay Ridge neighborhood.

[26][27][28] As part of the Metropolitan Transportation Authority (MTA)'s 2010–2014 Capital Program, funding was provided for a 25-station renewal program, which focused on renovating stations with a high concentration of components rated 3.5 or worse on a five-point scale, with 5 being the highest.

[38] The decision to remove a lane from Fourth Avenue for the construction of the elevator was criticized by members of the local community board who believed that the change would be unsafe for pedestrians.

[35][40] In order to provide space for one of the new staircases to the platform, the station's longtime vendor lost its lease in February 2017.

[37][41] A second staircase was added from the mezzanine to the southwestern corner of Fourth Avenue and 86th Street as part of the project.

In addition, the station agent booth was modified to a wheelchair-friendly height, and railings, turnstiles, platform panels, Braille signage, and powered gates were reconfigured to provide full accessibility.

[46] However, because of resource shortages caused by the COVID-19 pandemic in New York City, completion was pushed back to July 29, 2020.

[52][53] The track walls had their mosaic tiling restored as part of the station's 2011 renovation.

[54][52] The southern section of the station is where the platform was extended in 1970, and they have no mosaic trims or tiles along the wall, instead including an extension of the tunnel benchwall.