The shooting happened in the Chatham neighborhood near the 87th Street Red Line stop about 6:10 a.m. Saturday, police said.
The victim was transported to the University of Chicago Medical Center in critical condition, police said.
The man died just after 4:50 a.m. Sunday, according to CPD.
SEE MORE: Chicago shooting: Man, 60, critically hurt after shot during argument on CTA Red Line, police say
Police said the shooter fled from the train at 87th Street. No one is in custody and Area Two detectives are investigating.
The man killed was not immediately identified.
Crime on the CTA is becoming all too common, riders say.
CTA rider Raymond Head said he's forced to take the train daily to work.
"I got to get home and make the money for my kids, so I'm trying to stay safe myself," he said.
The video in the player above is from an earlier report.