The incident happened at about 7:35 a.m. on the east side of the station, police said.
The bicyclist, 37, suffered serious injuries and was awake when he was taken to the hospital, police said.
By 9:41 a.m. MDW inbound and outbound trains were on the move after train #2203 struck a person.
Extensive delays are expected Thursday morning.
The crash happened one day after the village's "Bike to Metra Day."