Despite the name, the station is located in the neighborhood of Fort Hamilton (as its original name implied) at the intersection of 95th Street and Fourth Avenue in southwestern Brooklyn.

On August 25, 1922, the Transit Commission directed its chief engineer, Robert Ridgeway, to plan an extension of the Fourth Avenue Line from 87th Street to Fort Hamilton.

[5] On September 12, 1922, a meeting was held by the Transit Commission to determine whether a stop at 91st Street should be included as part of the planned extension.

"[11] As part of Contract 11B, the extension was built with two tracks, with the exception of a short three-track stretch just north of the terminal at 95th Street.

[13] As a result of a motion made by Commissioner LeRoy Harkness in front of the Transit Commission, the contract was set to be put back up for bid.

[14] On November 2, 1923, the Board of Estimate approved the contract for the line with T. A. Gillespie Company, the same contractor that had bid on the project earlier, but withdrew.

[16][17] The final extension to 95th Street, Route 18, opened on October 31, 1925,[3][16] with the first train leaving at 2 p.m.[3] The city government took over the BMT's operations on June 1, 1940.

[21] On July 14, 1967, the NYCTA awarded a contract to conduct test borings at eleven stations on the Fourth Avenue Line, including 95th Street, to W. M. Walsh Corporation for $6,585 (equivalent to $60,172 in 2023) in preparation of the construction of platform extensions.

[24] As part of a plan to increase accessibility in the New York City Subway, during the early 1990s, the MTA proposed installing elevators at the Bay Ridge–95th Street station by 2010.

[28] In December 2022, the MTA announced that it would award a $146 million contract for the installation of eight elevators across four stations, including Bay Ridge–95th Street.

[48] The station is built on the west side of Fourth Avenue due to plans for a possible extension of the express tracks south of 59th Street.

[54] A groundbreaking ceremony was held by New York City Mayor John Hylan on April 14, 1923 in Bay Ridge[55][56] and in Staten Island on July 19.

[57] Officially, the plan was delayed due to lack of funding,[59][60] but Hylan and New York City Board of Transportation (BOT) Chairman John Delaney also wanted to secure freight service for the tunnel.