The schoolboys were detained when counter terrorism officers moved in on the North Yorkshire market town of Northallerton in October 28.
The two defendants, aged 14 and 15, made their first appearance before Leeds Crown Court today.
The pair face a joint allegation of conspiracy to murder.
The 15-year-old is also charged with unlawful wounding and aggravated burglary.
None of the charges were put to the boys.
They spoke only to confirm their names, dates of birth and to confirm their identities as British.
At an earlier magistrates hearing, lawyers for both boys indicated that not guilty pleas would be entered in due course.
The prosecutor at the earlier hearing said the charges were a result of an ‘extremely disturbing series of events’.
The parents of both defendants sat in the public gallery throughout the 20-minute hearing.
A trial date was set for May 2 next year.
Both boys will next appear before the court on February 12 when they are expected to enter pleas to the charges.
Arrangements were also made for the defendants to give recorded evidence prior to a trial.
No applications for bail were made and both were remanded into secure youth accommodation until their next court appearance.