Mark Bridger, 46, was seen in Caernarfon Crown Court on Wednesday, nine days after April, from Machynlleth, Powys, went missing.
No members of April's family were in court for the hearing.
Mark Bridger Mark Bridger is accused of murdering and abducting five-year-old April Jones
Mr Bridger, from Machynlleth, is also charged with attempting to pervert the course of justice.
The latter charge refers to the unlawful disposal and concealment of a body.
Police say the search for April will continue at the same intensity for another fortnight
Mr Bridger was wearing a black jumper over a grey t-shirt and spectacles for the video-link appearance from HMP Manchester.
He confirmed his name and that he could hear the proceedings.
The judge, Mr Justice Griffith Williams, asked if he understood what had been discussed and Bridger replied: "Yes, sir".
There was no application for bail and he was remanded in custody to appear in a plea and case management hearing on 11 January.
April was last seen outside her home in Machynlleth on Monday 1 October and has not yet been found.
Police said on Wednesday they were extending the current search for her to a radius of a few miles around Machynlleth.
Source: BBC news