The accident occurred in the school gymnasium when the teenager was rope-climbing. He managed to climb up a little way and then slipped down and died soon after.
"The teenager's mother said he suffered with health problems," Irina Melnik said. "The circumstances of the incident are being established."
Russia and CIS countries have been plagued by a series of fatal accidents during physical education lessons. Earlier this year a 15-year-old boy from Ufa, the capital of the Republic of Bashkiria in southwest Urals, died during a ski race.
On November 5, the government of neighboring Ukraine banned school children from taking part in cross country runs without prior medical checks after five children aged between 12 and 15 died during PE lessons in October and early November.