The charge follows the death of the 11-month-old Paynesville boy on Tuesday evening. Emergency services were called to the Digney Street home following reports of an unresponsive baby.
Police said he was taken to Bairnsdale Hospital but died a short time later.
Homicide Squad detectives charged the 26-year-old man this afternoon.
He is due to appear in the Bairnsdale Magistrates’ Court later today.