The student, who did not want to named for fear of “stigmatised even more”, told his headmaster he was growing the facial hair for religious purposes.
When recalling the conversation he had with his headmaster, the 21-year-old, from Saint Denis, Paris, said: “The Prophet was wearing one. It is something important to me.
“He [the headmaster] gave me a few days for reflection to see if I change my mind and shave [the beard… but I will not!”
The student is the son of a non-practicing Muslim and an atheist.
He admitted to missing lessons to go to Friday prayers and did not shake the hands of his fellow pupils for “decency” reasons.
The unnamed pupil said he had previously agreed to stop wearing harem pants at his headmaster”s request as he agreed they could be interpreted as a religious dress wear.
Religious symbols in schools were banned in 2004 due to French values which say there must be a separation between the state and religious activities – however beards are not part of the legislation.
The pupil said: “I am not the only one with a beard, both among students and teachers.”
He added that he had received support from some of his classmates.
One girl claimed the complaints had left “everything mixed up”.
In the past year, France has been gripped by a series of bitter arguments about the separation of state and religion.
Over the summer, a number of towns tried to ban bikinis as it “overtly manifests adherence to a religion at a time when France and places of worship are the target of terrorist attacks”.
The ban has since been quashed by France”s top administrative court.