Around 60 people turned up for the start of the school year outside the gates of the Athenee Royal of Antwerp school, where most students are Muslims, carrying banners calling for freedom of choice, television pictures showed.
Among the protesters several young girls wore long black or white veils, coloured scarves or party hats.
Another 70 protesters assembled at the Hoboken secondary school, also in Antwerp.
"This ban is against the freedom of religion and violates the right to an education for young Muslims”, said Samira Azabar, one of the protest organisers.
After the two schools decided on the ban in June an imam in Antwerp called on all Muslim parents not to send their children back to school for the new academic year.
Athenee head mistress Karin Heremans said that so far a dozen students decided not to return to school.
She justified the ban by saying that girls who had refused to wear the Muslim veil had been subjected to intimidation at a school where "the proportion of Muslims has increased from 50 percent to 80 percent in the last three years."
The Belgian state is "neutral" rather than secular, leaving the decision on banning or allowing veils to school authorities.