The free transfer between the Eastern Parkway and Franklin Avenue shuttle platforms was added in 1999 using a passageway that had existed since October 1928, when the BMT Botanic Garden station opened.

Contract 2 extended the original line from City Hall in Manhattan to Atlantic Avenue in Brooklyn.

[17] The New York City Board of Transportation announced plans in November 1949 to extend platforms at several IRT stations, including Franklin Avenue, to accommodate all doors on ten-car trains.

Although ten-car trains already operated on the line, the rear car could not open its doors at the station because the platforms were so short.

[23] In April 1993, the New York State Legislature agreed to give the MTA $9.6 billion for capital improvements.

Some of the funds would be used to renovate nearly one hundred New York City Subway stations,[24][25] including Botanic Garden.

Support in the Bedford-Stuyvesant and Crown Heights communities persuaded the city to rebuild the line from July 1998 to September 1999.

[23] Prior to the rehabilitation project, only a portion of the station was in the tunnel, as the platforms were longer and continued outdoors.

The Botanic Garden station on the BMT Franklin Avenue Line has two tracks and two side platforms.

At street level, it features floral wrought iron fencing in recognition of its location near the Brooklyn Botanic Garden (entitled IL7/Square by Millie Burns).

To the immediate north of the station, the 1878 railroad tunnel that carries the line under Eastern Parkway has been dramatically lighted.

[31] Both platforms have yellow i-beam columns on both sides at regular intervals with every other one having the standard black station name plate in white lettering.

The platform walls have their original Dual Contracts trim line with "F" tablets for "Franklin" at regular intervals.

At the extreme west (railroad north) end, the platforms were extended in the 1950s to accommodate the current standard IRT train length of 510 feet.

The station has been adopted by Clara Barton High School as part of New York City Transit's Adopt-A-Station program.

[30][35] This junction is a severe traffic bottleneck, primarily during rush hours, and rebuilding it would require massive construction including the tearing up of Eastern Parkway.

The plan was first unveiled in the 1967 Transportation Studies for Southeast Brooklyn, and subsequently in 1968 as part of the Program for Action.