It was the second police-involved shooting just hours apart in New York City.
It happened at the 225th Street Station in the Wakefield section, after someone called 911 saying a man was firing shots.
Police were also alerted by their ShotSpotter system.
Authorities say both plainclothes and uniformed officers arrived at the scene, encountered the gunman, and fired multiple rounds at him.
He was shot in the shoulder and was taken to Jacobi Hospital, where he is listed in stable condition.
Police released a photo of the semiautomatic pistol they say the man had in his possession on the southbound platform.
The officers involved were also being evaluated.
"Our officers never hesitate to run towards danger every day to protect our city," NYPD Transit Chief Edward Delatorre said. "This morning's shooting just underscores the danger that these officers have to live with and the necessity to get illegal weapons off the streets."
Police haven't identified the suspect, but they say he has an extensive criminal history.
The station was closed for the police investigation.
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