[12] Under the revised plan, the four-track tunnel under Eastern Parkway was to be double-decked, except at the Franklin Avenue station, where all tracks would be on the same level.

[16] The tunnel between Grand Army Plaza and Nostrand Avenue was built using the cut-and-cover method, with two steam shovels excavating an estimated 600,000 cubic yards (460,000 m3).

[26] In 1981, the MTA announced the creation of its Culture Stations program to install public art in the subway.

The Culture Stations program was started to deter graffiti, and was inspired by legislation in the New York City Council that mandated that 1% of the cost of constructing public buildings be used for art.

Four stations, namely Eastern Parkway–Brooklyn Museum, Astor Place, 66th Street–Lincoln Center, and Fifth Avenue/53rd Street, were selected for the program due to their proximity to cultural institutions.

[32] The station subsequently underwent a renovation that lasted between 13 and 15 months;[33][34] the project was expedited in advance of the museum's anniversary.

[33] As part of the 2015–2019 MTA Capital Program, elevators were added to the platforms and street, which made the station fully compliant with accessibility guidelines under the Americans with Disabilities Act of 1990.

[41][42] Designed by Urbahn Architects and constructed by Gramercy Group, the project cost $25.8 million and included three elevators and a rebuilt staircase.

In the eastern mezzanine are architectural ornaments from the Brooklyn Museum collection, installed during the 2003 renovation of the station.

[33] The platforms and the eastern mezzanine formerly displayed abstract art paintings created in 1991 by artist Pat Steir, collectively called the Brueghel Series.

One exit is on the south side of Eastern Parkway, in front of the Brooklyn Museum; the elevator is located by this entrance.