The Lincoln County, S.D., Grand jury indicted Joseph Patterson, 27, on one count of second degree murder, two alternate counts of first degree manslaughter, aggravated battery of a infant and felony child abuse in the death of Tyrese Ruffin, State's Attorney Tom Wollman said.
Police say Patterson was alone with the child at a Sioux Falls apartment.
Ruffin was unresponsive when he was hospitalized, and doctors determined head injuries were the result of an assault, not an accident, KELO-TV, Sioux Falls, reported.
Authorities did not identify the child's mother but confirmed the father is Minnesota Vikings' Adrian Peterson.
The suspect Patterson pleaded guilty to domestic assault and violating a no-contact order in 2012. His girlfriend, who is not Ruffin's mother, wrote that Patterson had threatened to kill her, and severely spanked her son, 3.