West Midlands Police said the three-month-old boy was found by paramedics in cardiac arrest at a home in Stoke, Coventry, on 29 June.
He had suffered a “catastrophic” head injury and was pronounced dead two days later in hospital, the force added.
James Scott – who police say knew the child – appeared at Coventry Magistrates’ Court and is due to appear at Warwick Crown Court on Tuesday.
Police said Scott, from Coventry, was arrested at the time but released under investigation “while complex and extensive enquiries were carried out”.
He was remanded in custody after his appearance before magistrates on Friday.