It happened at the CTA station at 55th and the Dan Ryan.
The Cook County Medical Examiner's office has identified the man as George Lash, 19.
After processing the scene, police re-opened the station around 7 a.m. Overnight, CTA used shuttles to transport passengers between 47th Street and 63rd Street.
Police say they were notified around 1:40 a.m. that a man was brandishing a gun at the Garfield station. The train conductor reportedly directed the police officers to the train where the offender was last seen. A struggle between two officers and the offender ensued, during which police say the offender pointed his gun at them. That's when both officers shot the man.
The suspect was rushed to Stroger Hospital in critical to serious condition but later died from his injuries.
"Unfortunately, the events lead to a life being lost, but you know, when you try to murder police officers, that's what's gonna happen. I'm really glad our officers are safe. We took a dangerous person off the street," said Chicago Police Department Supt. Jody Weis. "Here he is riding on the train with a gun."
No other injuries were reported, and police say a weapon was recovered at the scene.
The Independent Police Review Authority is investigating the shooting.
(The Associated Press contributed to this report.)