Mikaeel Kular's body was found in Fife in January, after he had been reported missing from his home in Edinburgh.
It was reported the death certificate was released by a registrar in Kirkcaldy.
His mother, Rosdeep Kular, 33, has been charged with his murder and is remanded in custody.
She appeared in private at Edinburgh Sheriff Court under her married name of Adekoya, where she made no plea or declaration to the charges. She is also accused of attempting to defeat the ends of justice.
The death certificate said he had been found dead at 4.02am on January 18.