Mark Bridger, 46, stood in the dock of Aberystwyth Magistrates' Court as the charges were put to him.
Bridger is also charged with the unlawful disposal and concealment of her body with intent to pervert the course of justice.
Bridger cried 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 today's hearing.
The court clerk read out each charge individually, asking Bridger if he understood.
When the murder charge was read out he answered "yes" with a tremor in his voice and tears in his eyes.
He answered "yes" twice more to confirm he had understood each charge.
When his name was read out, he said: "That is correct."
He answered "correct" to confirm that his date of birth was November 6, 1965, and said the same for his Mount Pleasant farmhouse address at the village Ceinws.
Bridger was brought into court wearing a blue jumper. His faced looked red and flushed and he was unshaven.
He gazed down at the floor inside the dock area of the court, enclosed in protective glass.
He did not make eye contact with anyone.
His eyes were tearful before he answered any questions and he appeared to be struggling to hold back his weeping.