Former lifeguard Mark Bridger, 46, stood in the dock as the charges were put to him.
As well as abducting and murdering April, Bridger is charged with the unlawful disposal and concealment of her body with intent to pervert the course of justice. Bridger cried to himself as he spoke to confirm his name, age and address. He also confirmed he understood the charges.
Bridger appeared on the verge of tears throughout the hearing, which lasted around four minutes. He was remanded in custody and will next appear at Caernarfon crown court on Wednesday.
April, who suffers from cerebral palsy and needs daily medication, was last seen near her home on the Bryn y Gog estate in Machynlleth on Monday evening.
Bridger was arrested the following day.
There were angry scenes outside the court as the van carrying Bridger arrived for the hearing.