Both defendants appeared before Leeds Crown Court with their parents watching from the public gallery.
The boys aged 14 and 15 were arrested by counter-terrorism officers in Northallerton on 28 October.
The older youth is also charged with unlawful wounding and aggravated burglary.
The pair, who cannot be named, were remanded into secure youth justice accommodation.
They were initially arrested on suspicion of preparing an act of terrorism at a school.
Searches were carried out at a number of properties in the market town.
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