The 51-year-old employee was on the street in the 7500-block of North Paulina Avenue at about 9:11 p.m. when police said someone inside a white SUV started shooting.
The CTA employee was shot in the chest and transported to St. Francis Hospital, where he was listed in serious condition.
The shooter fled the scene and is not in custody, police said. Area Three detectives are investigating.
CTA President Dorval Carter released a statement saying, "This evening, we've learned of yet another violent criminal act involving the use of a gun, this time injuring one of our own.
"We are both saddened, and also in disbelief that we are once again having to address the topic of gun violence and public transit.
"An on-duty Rail Operations employee (switch worker) was standing outside the terminal when an unknown vehicle drove by striking a nearby vehicle and the employee. The employee was transported to a nearby hospital in serious condition.
"CTA will make support services and resources available to employees affected by this latest event.
"We are working closely with local law-enforcement, and assisting in whatever way we can, including reviewing, and providing any relevant security camera footage. Further, CTA will hold those responsible to the fullest extent of the law."