An entire section of the two-storey building housing the school in Belyayevka, 120 km (75 miles) from the regional capital Orenburg in the southeastern Urals, came crashing down, spreading debris over a wide area.
Local people rushed to help firemen and police trying to rescue children from the rubble, and emergency workers sent from Orenburg brought in a crane to help remove the piles of debris.
"Eleven children have been taken out of the rubble, five of them are dead, four are injured and 800 people were evacuated," an Emergencies Ministry spokeswoman in Orenburg said. The death toll was not expected to rise, she added.
The collapse exposed a children's map of the region and a poster in memory of local war heroes on the inner walls of what had been the stairwell.
The school catered for children aged between 7 and 17.
Prosecutors opened a criminal investigation into the accident for possible violations of building safety regulations, while experts tried to identify the main point of weakness in the fabric of the building, constructed in 1962.
"The main load-bearing wall of the building collapsed, not the stairwell. The accident was not caused by roof maintenance, but may have been linked to the removal of old windows," said Angelika Linkova, an official in the local prosecutor's office.
Cracks were visible in the remaining walls of the school, where windows were being replaced before the building's partial collapse, said a photographer at the scene.
Many Russian schools and other public buildings are decaying after decades of neglect, though the Kremlin has pledged to renovate buildings in poor condition.
Two years ago, 45 women perished in a fire at a Moscow drug treatment centre. Days later, 62 elderly people and staff members died in a nursing home fire in South Russia.
They were the worst in a series of accidents blamed on the poor state of public buildings.