CPD said the battery was reported just after 5:10 a.m. in the 1200-block of North Clark Street.
The victim was riding the Red Line when an unknown male suspect, who police later identified as Curtis Tyler, came up and hit him with a hammer, Chicago police said.
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The man suffered a laceration to the forehead and was taken to Advocate Illinois Masonic Medical Center, where he was stabilized.
Tyler was arrested just after 6 a.m. Tuesday in the 900-block of West Belmont Avenue in Lakeview.
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He was charged with aggravated battery, theft, carrying a weapon on the CTA and public indecency, police said.
He's next due in court Wednesday.
Howard-bound Red Line trains had some delays after the incident.