The man, 53, was arguing and fighting with another 53-year-old man at the stop in the first block of West 95th Street about 1:55 a.m., Chicago police said.
He was walking down stairs when the other man shot him in the back, abdomen and lower left leg, police said.
He was taken to the University of Chicago Medical Center, where he was in critical condition, police said.
The second 53-year-old man was taken into custody and a weapon was recovered at the scene.
Red Line service was temporarily suspended between 95th and 87th due about an hour later to police activity, according to CTA.
Trains were running with residual delays as of 4:50 a.m., according to CTA.