It is located roughly at the intersection of Broadway, Fulton Street and Van Sinderen Avenue at the border of Bedford–Stuyvesant, East New York and Bushwick.

Lexington Avenue and Fulton Street trains were through-routed, going around the East New York Loop, with service to Cypress Hills requiring a transfer.

In 2017, the New York City Economic Development Corporation started studying options to rezone the surrounding area as a transit hub.

The line opened as the Brooklyn and Jamaica Railroad in 1836, under lease to the LIRR, but did not include a station at East New York until early 1843.

[7] The Brooklyn and Rockaway Beach Railroad (the predecessor to the BMT Canarsie Line) began service in the area in 1865.

[14] This connection, equipped with a third rail to supply electric power, was opened on August 9, 1900, and new service patterns were implemented: during times other than rush hours, Lexington Avenue and Fulton Street trains were through-routed, and travel beyond Manhattan Junction required a transfer.

[8]: 14 [22]: 385  The full BMT 14th Street-Canarsie Line was completed on July 14, 1928, with the opening of the segment connecting Broadway Junction with Montrose Avenue.

Further eastward extension of the line was delayed by World War II; the Broadway–East New York station opened on December 30, 1946.

[25][26] A direct escalator passageway was constructed between the IND and BMT stations in East New York to allow passengers free transfers.

[28]: 16, 38  The Fulton Street Elevated was now redundant, and BMT service on the line closed entirely on April 26, 1956, with the eastern portion to Lefferts Boulevard connected to the IND.

[35]: C-24–C-26  As part of the project, an abandoned mezzanine and adjacent staircases were removed, a new station booth was built and the public address system was improved.

In 2001, as part of the work a piece of artwork made by Al Loving titled Brooklyn, New Morning was installed in the station.

[36] This piece of art consists of 75 unique glass panels arranged in a series throughout the complex and a mosaic mural wall that is 7–10 feet (2.1–3.0 m).

[39] As part of a project initiated in 2017 in which 200 blocks of land in East New York were rezoned for housing and improvements to area parks and schools were planned, the New York City Economic Development Corporation initiated a study to foster economic growth around Broadway Junction as a transit hub with residential and commercial uses.

[42] Mayor Eric Adams announced in May 2023 that the MTA would spend $400 million on improvements at the Broadway Junction station, including seven elevators, a new entrance on Van Sinderen Avenue directly to the Canarsie Line platforms, and replacement of all of the complex's escalators.

[45] Plans for the Interborough Express, a light rail line using the Bay Ridge Branch right of way, were announced in 2023.

[52] Calls for elevators were renewed in 2017, after the announcement of the L train shutdown in 2019–2020, which temporarily restricts Canarsie Line service to Manhattan during off-peak hours.

[54] The station house is adjacent to Callahan-Kelly Playground, and is recessed a short distance west from Van Sinderen Avenue.

[8]: 38 [49]: 95 A ventilation structure for the IND line sits at the west end of the park at Sackman Street.

[24][23] The station is one of the highest elevated platforms in the city, sitting above the already-elevated BMT Jamaica Line.

[57]: 32, 64  During 1999, this station underwent a series of renovations, including new canopies, a new crossover (known as "The Barn" because of its rustic red siding and white trim), and the removal of a hazardous crossunder.

A second fare control area, a mezzanine, at Conway Street in the middle of the platforms was also closed, and was removed in the 2000s as part of the station's renovation.

[8]: 50  The mezzanine is above the platforms and connects to the Canarsie Line and to the exit at street level via two long escalators.

[8]: 49  Some of the land was given to the New York City Parks Department in 1945 for the construction of Callahan-Kelly Playground, which was named after two local soldiers who died during World War I.

[55] The station was nearly complete when the United States' entrance into World War II in 1941 halted construction due to material shortages.

[8]: 14 [25][26] Work resumed following the war to install the necessary signals, tracks and complete the escalators to the BMT platforms.

[67][68][69] The station's tile band is unique in that it incorporates two types of tile–gloss and matte–in contrasting shades of cobalt blue (gloss border) and blueberry (matte center).

[72] East of the station, the tunnel widens on both sides to accommodate an additional trackway diverging from the local tracks.

The severed connection between the station and the East New York Yard can also be seen below the Canarsie Line and above the north side of Fulton Street.

[3] Due to the COVID-19 pandemic in New York City, ridership dropped drastically in 2020, with only 1,292,868 passengers entering the station that year.