Joseph Patterson turned himself in Tuesday. The Minnehaha County Sheriff's Office had issued an arrest warrant.
Patterson was released on a $2 million bond in September. He's charged with second-degree murder, manslaughter and aggravated assault in Tyrese Ruffin's 2013 death.
Patterson also faces aggravated assault and kidnapping charges in an alleged attack on Tyrese's mother in June.
Patterson was living with Tyrese's mother when he called 911 and reported the boy had stopped breathing. Doctors determined Tyrese's injuries couldn't have been accidental.
Prosecutors say Patterson beat him. Patterson maintains Tyrese choked on a snack.