Michael Korosa has been charged with involuntary manslaughter and aggravated battery of a transit employee in the incident.
Chicago police initially said Korosa was charged with murder.
He was arrested Saturday in Chicago, police said.
On Aug. 10, Korosa battered Elijah Flores, leading to fatal injuries in the 500-block of West Lake Street, at the Clinton Green Line station, officials said.
Police say the 9-year-old boy was with a 22-year-old man who got into an argument with two others along the Green Line.
Those two suspects chased after the man and Flores. That's when police say an object was thrown at them, causing both to fall down the stairs.
Korosa is due in court Monday.
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