The Morgan Avenue station opened on December 14, 1928, as part of an eastern extension of the Canarsie Line from Montrose Avenue in Brooklyn, which opened four years earlier, to Broadway Junction, connecting afterwards to the already-operating elevated line to Canarsie.
There are two tracks and two side platforms. Both platforms have their original BMT style mosaic trim line and name tablets that are predominantly earth tones of brown, tan, orange with white accents. There are "M" tablets for "Morgan" on the trim line at regular intervals. There are also directional mosaic signs in the same style as the name tablets.