24-year-old Robert Harford was arrested Wednesday night after being interviewed by detectives.
His infant daughter, Ava Harford, died Tuesday night at Maine Medical Center.
She was originally brought to the hospital Sunday night. She was unresponsive when she arrived.
An autopsy revealed that she died of multiple blunt force head injuries.
Harford lived with Ava and her mother, 25-year-old Kirby Gushee.
Robert Harford is expected to make his first court appearance in Knox County Superior Court on Friday.