Mark Bridger, 46, was arrested the day after April went missing from near her home in Machynlleth, mid Wales, on Monday evening (local time), BBC reports.
Bridger, who has also been charged with attempting to pervert the course of justice and child abduction, is due before magistrates in Aberystwyth on Monday.
Dyfed-Powys Police said they remained "focused and committed" to finding April.