Adam Lewis, of Fairmead Avenue, went before the bench to face charges for murder and two counts of rape between May 15 and May 20.
The 18-year-old is also charged with arson with intent to endanger life at a house in Orchard Road, Moreton, on May 12.
Hannah's body was found on Bidston Hill on Saturday in undergrowth near the Observatory following a call from a member of the public.
A post-mortem examination revealed she died as a result of multiple injuries
Lewis will appear at Liverpool Crown Court on Friday, May 25, with preliminary hearing scheduled for June 6.
THE GLOBE