A spokesman from union NAHT, which represents headteachers, said kids were being told that going to protests in school hours was "simply unacceptable".
"It will be treated as truancy and the schools' disciplinary sanctions will apply.
"Either they will be given a detention or a fixed-term exclusion."
It comes after lessons were disrupted by protesting pupils when the war kicked off earlier this year.
Mr Bush's visit starts on Tuesday.
Extra police are at ports and airports, and have been checking people arriving on Eurostar trains from France, after recent warnings of terrorist attacks.
Mr Bush will also be bringing hundreds of armed guards with him from the US.