The 14-year-old boy, who has not been named due to his age, appeared at Cardiff Magistrates’ Court in South Wales speaking only to confirm his name.
District Judge Stephen Harmes told the defendant he would next appear at Cardiff Crown Court.
Logan – also known as Logan Williamson – was found dead in Ogmore River near Pandy Park in Bridgend after police were called following reports of a missing child at 5.45am on 31 July.
He was taken to the Princess of Wales Hospital, where it was confirmed he had died.
Senior investigating officer, Detective Chief Inspector Mark O’Shea, said: “This is a very harrowing case for all involved and I extend my deepest sympathies to Logan’s family and friends.
“This remains an extensive and sensitive investigation by the Major Crime Investigation Team and I am grateful to the local community for its support and understanding while we have continued to gather evidence across several scenes.”
Logan’s mother Angharad Williamson, 30, was also charged with murder today, making her the third person accused of involvement in the boy’s death, after her partner John Cole, 39, was charged in August. She will appear in court tomorrow.
Both Williamson and Cole are also accused of perverting the course of justice.
A provisional trial date for all of the accused has been set for 31 January next year with a time estimate of four weeks.