The pupil, who was studying at Charlemagne school in the Marais district of central Paris, fell to his death shortly after 8am, just after the bell had gone to start the day.
The exact circumstances around his death and how he managed to fall remain unclear.
Firefighters were called to the school in the fourth arrondissement after reports of a pupil falling 15 metres.
He was suffering from cardiac arrest when the paramedics arrived, but they were unable to save him and he died later of his injuries.
Later that day the headteacher of the school sent an email to all parents to alert them of the tragedy, but it did not go into detail about what happened.
“The school has just been struck by a horrific incident…” said headteacher Christophe Hespel. “This tragedy has hit the devastated family, but also the pupils and the staff who feel immense sadness.”
Education authorities have offered psychological support to anyone affected and police in the French capital have launched an investigation.
Following the incident some pupils reportedly took to Twitter and suggested the death may have been a suicide.
“The authorities in Ile de France (Paris region) will wait for the conclusions of the investigation and will draw any lessons, if necessary, from this tragedy,” said Agnes Evren from the regional education board.