Nineteen-year-old Ronald Cuff Jr. of Vineland also faces an aggravated assault charge and two counts of child endangerment in the indictment recently handed up by a Cumberland County grand jury.
The baby's mother, Melina A. Vega, was indicted on two counts of child endangerment.
Prosecutors say the charges stem from the death of the couple's 2-month-old son.
They say Cuff repeatedly shook the child while caring for him, and the boy's maternal grandmother took him to a hospital. The child died a week later.
Cuff remains jailed on $250,000 bail. He could not be reached for comment Sunday, and it was not known if he had retained a lawyer.