The current configuration dates from a 1956–1961 reconstruction project to straighten the platforms and eliminate a level junction north of the station, which had caused a switching bottleneck.

[5][6] Contracts for the Fourth Avenue Line were awarded on May 22, 1908, for the section between 43rd Street and the Manhattan Bridge, but the Board of Estimate did not approve them until October 29, 1909, when a taxpayer's lawsuit regarding the city's debt was settled.

[7][8] The Fourth Avenue Line was assigned to the BRT (after 1923, the Brooklyn–Manhattan Transit Corporation or BMT[9]) in the Dual Contracts, adopted on March 4, 1913.

After the Montague Street Tunnel was approved,[14] the planned station was changed to an express station that could serve trains from both the Manhattan Bridge and the Montague Street Tunnel (there would still be two bypass tracks for Fourth Avenue express trains using the bridge).

[14][16] The commission also requested bids for the addition of crossovers, allowing trains from the tunnel or the bridge to stop at DeKalb Avenue.

[24] In 1922, the New York State Transit Commission directed its engineers to prepare plans for lengthening the platforms at 23 stations on the BMT's lines to accommodate eight-car trains.

[25][26] Though the Transit Commission ordered the BMT to lengthen these platforms in September 1923,[27] no further progress was made until February 16, 1925, when the New York City Board of Transportation (BOT) commissioned its engineers to examine platform-lengthening plans for DeKalb Avenue and eleven other stations along the Fourth Avenue Line.

[28] The New York City Board of Estimate appropriated $362,841 for the lengthening of the platforms at DeKalb Avenue and five other stations in January 1926[29][30] and awarded the contract to Charles Meads & Company early the next month.

A group of level crossovers at the northern end of the station allowed all tracks access to both sides of the Manhattan Bridge and to the Montague Street Tunnel.

The Fourth Avenue local tracks led straight onto the Manhattan Bridge west of the station, while the Brighton line tracks led straight to the Montague Street Tunnel, so the crossovers allowed trains from both lines to switch between the bridge and the tunnel.

[38][39] By then, the original track layout caused many train delays on the Fourth Avenue and Brighton lines.

[40] On November 30, 1955, the New York City Transit Authority sent a recommendation to the Board of Estimate for the approval of a $13,152,831 contract to eliminate the bottleneck.

[41][42] The Citizens Budget Commission recommended that the appropriation be canceled, but three other civic groups opposed the elimination of the funding.

A diamond crossover north of the station had caused frequent bottlenecks, but was removed during the realignment and replaced with two flying junctions.

When the Chrystie Street Connection opened in 1967, the station became a transfer point for trains to and from the IND Sixth Avenue Line.

[49] In the early 2000s, architect Lee Harris Pomeroy designed a renovation of the DeKalb Avenue station.

The plans included adding elevators for ADA accessibility, as well as restoring the original station tiles and mosaics.

The MTA repaired the staircases, retiled the walls, added new tiles to the floors, upgraded the station's lights and public address system, installed ADA yellow safety treads along the platform edge and replaced the trackbeds for all trains entering or bypassing the station.

Outside of the turnstile bank is a token booth, a single street stair to the southwest corner of DeKalb Avenue and the Flatbush Avenue Extension built inside a store front, and two staircases that meet at their landings and an elevator that go up to the southeast corner outside a former Applebee's restaurant.

B and D trains use the north side of the bridge via the Chrystie Street Connection to the IND Sixth Avenue Line.

[44] Also south of this station, there is a bellmouth where the northbound track of the Brighton Line curves northwest onto Fulton Street.

South of this station, a junction was built at Fulton Street for a never-built branch to run via Lafayette Avenue and Broadway.