The younger boy, 15, appeared first by videolink from Feltham Young Offender Institution and spoke only to confirm his identity.
Later, the 16-year-old appeared in the dock and confirmed his identity.
Judge Lucraft confirmed the timetable for the case and remanded him in custody too.
Members of the victim’s family sat in court for the short hearings.
Kelyan was attacked on a London bus on the way home from school in Woolwich, south-east London, on 7 January.
Police were called at about 14:30 GMT to reports of a stabbing on the Route 472 bus on Woolwich Church Street.
Prosecutor Tom Little KC told the hearing earlier that the victim was sitting at the back seat of the bus when two people both armed with “lengthy machetes” attacked him.
Despite the efforts of the bus driver, passengers and attending paramedics to save his life, Kelyan was pronounced dead shortly after being attacked.
