When the Brooklyn and Jamaica Railroad opened in April 1836, under lease to the LIRR,[4]: 44  it did not include a station at East New York.

It was initially at grade level where the lines crossed, but was placed in a tunnel in 1915; the platforms, under East New York Avenue, still exist.

[14] In 1924, the station was the location of a firework accident that resulted in Palsgraf v. Long Island Railroad Co., an oft-cited court case on the doctrine of proximate cause.

[15][16][17] In the 2010s, many locals and elected officials such as Brooklyn's then-borough president, Eric Adams, advocated for renovations to the station, including bringing it into compliance with the Americans with Disabilities Act of 1990.

[13][14] On either side of the station, the tracks descend into a tunnel, allowing the main lanes of Atlantic Avenue to return to the surface.