The youths were allegedly caught in possession of bayonet-style knives near a prayer hall in the Sydney suburb of Bankstown.
One of the boys allegedly had a handwritten note pledging allegiance to the so-called Islamic State.
Police charged both with planning an act of terror and being members of a terrorist organisation.
On Thursday (Oct 13), bail was refused in Parramatta Children's Court.
Their cases are adjourned until December, but if convicted the 16-year-olds potentially face life behind bars.
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