Willie Strong, 30, was being held on $100,000 bond, the Chicago Tribune reported.
Prosecutors said the child, Jayshaun, and his 2-year-old brother, were left with Strong when their mother left for school at about 8:30 a.m. Sept. 24. When the mother, whose name was not reported, came home at about 3:30 p.m., she found the boys still in the tub, and Jayshaun was floating face up with his eyes open.
She began performing CPR before the boy was taken to a hospital, where he was pronounced dead at 3:44 p.m., the Cook County medical examiner's office said.
Strong told police he put the children in the bath and "left them alone for about 10 minutes while he went to the living room to smoke a cigarette," assistant State's Attorney Rich Gleason said.
Strong was also investigated on allegations that he abused the same child in June, said Illinois Department of Children and Family Services spokesman Jimmie Whitelow.
Ohio bar shooting arrested, charged with murder
Attkisson leaves CBS News, reportedly over network's 'liberal bias'