The employee spotted the boy walking around the station in Lakeview about 2:50 a.m., CPD said.
He was taken to Illinois Masonic Hospital in good condition, as he did not have any injuries, police said.
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The boy's mother had called 911 and said her son was missing and was supposed to be with a babysitter nearby.
Officers took her to the hospital, where she was reunited with the child.
Chicago police said there were no charges filed in the incident.