Joseph Mitchell is accused of suffocating the child and attempting to kill his other children, ages 10 and 13, in September 2010.
Investigators said Mitchell, now 49, locked himself in a room and also attempted to take his own life in the family's home in the Hardscrabble Plantation subdivision.
Mitchell has been in custody ever since the incident but has never gone on trial because of dozens of continuances.
On Friday, Mitchell's attorney made it clear that he intends to fight the charges against him. He faces one count of first-degree murder and two counts of attempted murder.
Mitchell rejected a plea deal from the Durham district attorney that would have reduced the charge to second-degree murder and a 43 year sentence to avoid trial. Instead, Mitchell entered a not-guilty plea on all charges against him.
According to court records, Mitchell will use the defense of automatism, an unconscious state more commonly known as sleepwalking.
Investigators remain tightlipped on a motive, but have hinted at extreme financial stress as a factor.
Court documents show Mitchell had an extra marital affair, and his wife confirmed it during an interview. Mitchell's wife was at home at the time of the child's death, but she was unharmed.
Warrants revealed a detective said a mask in the family's house may have been used or touched by Mitchell at some point. Investigators also said Mitchell's older children told him they woke up with something over their faces and had to fend off their father.
Mitchell's trial is set for March 2014.