The agreement between Jason Young and Meredith Fisher to transfer custody was filed in a Wake County court Friday.
Fisher will have primary custody of Cassidy Young. Jason Young will have visitation every other weekend, during holidays, birthdays and summers.
Michelle Young was found beaten to death in her Raleigh home. She was pregnant at the time and Cassidy, who was 2, was found wandering near her mother's dead body.
Although Jason Young was never named a suspect in the murder, in December a judge ruled in the civil case against him, saying he "willfully and unlawfully" killed his wife Michelle.
The criminal case remains unsolved.