Mark Bridger, 47, also denies attempting to pervert the course of justice following her disappearance in Machynlleth, Powys, in October.
April went missing on 1 October, and her mother and father, Coral and Paul, were at the plea and case management hearing at Mold Crown Court on Monday.
Dyfed-Powys Police still have 16 teams involved in the search operation.
The defendant, of Machynlleth, also denies a charge of attempting to pervert the course of justice which refers to the unlawful disposal and concealment of a body.