Michael Buchanan, 23, could spend the rest of his life in jail.
He is being held without bond.
It happened at a North Raleigh townhouse complex, where neighbors have set up a memorial on the front steps.
According to court documents, the back of the 22-month-old's skull was fractured, causing a brain bleed.
Police were called Thursday by workers at WakeMed Children's Hospital to say child abuse was suspected.
The caller said the mother's boyfriend -- later identified as Buchanan -- was there with her and acting suspiciously.