The boys, both 15, from North Yorkshire, have both denied a joint charge of conspiracy to murder relating to a period between December 31 2016 and October 29, last year.
They have also each pleaded not guilty to a charge of intentionally encouraging or assisting an offence.
These charges allege that each defendant "did acts capable of encouraging (the other defendant) to commit the offence of murder, namely encouraging (the other defendant) to kill students and teachers at (a North Yorkshire school)".
They have also denied a charge of encouraging or assisting an offence believing it would be committed.
The older boy has denied one offence of the unlawful wounding of a teenage girl and another of aggravated burglary.
The boys, who are both in custody, are due to go on trial at Leeds Crown Court.
Neither of the defendants nor the school can be named.