The incident happened at the Rockaway Avenue station in Ocean Hill just before 11:15 p.m.
The victim, later identified as Freddie Weston, was shot on the mezzanine level of the station near the MetroCard machines.
An MTA employee in the booth heard a gunshot and went out and saw the man shot in the head.
He was rushed to Brookdale University Hospital where he was pronounced dead.
The suspect ran away and detectives did not immediately have a motive and no arrests were made.
Police extended the crime scene investigation from the subway station into the street as they searched for evidence.
NYC Transit President Demetrius Crichlow said subway stations have cameras, half the subway trains now have cameras, and it is only a matter of time until they get an image of the suspect.
Officials believe the shooting death was the seventh homicide in the transit system this year.
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