Dominique Margueritat, the headmaster of the Trégey Lycée in Bordeaux, says the 18-year old student came from Morocco.
The incident happened earlier this week.
A source close to the police investigation says the student and the teacher disagreed over interpretations of Arab-world personalities.
Police say the boy slapped and punched the teacher before being arrested.
He has now been charged with assault and will face court in coming months.
Margueritat denied earlier reports that the dispute was about religion.