The shooting happened at about 10:46 p.m. in the 1100-block of North Kostner Avenue on Thursday.
The boy was with in a car with his mother when a man in a pickup truck pulled up and started shooting, police said.
The 3-year-old was taken to the hospital in good condition with a graze wound to the left leg, police said.
Jose Sanchez of Evanston was arrested on Friday, police said on Sunday.
The 42-year-old was arrested around 8:43 p.m. in the 4500-block of Cermak Road, according to police.
Sanchez has been charged with aggravated battery discharge of a firearm. He was scheduled to appear in court on Sunday.
Police said the boy's father was in a dispute with Sanchez before Thursday's shooting.
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