Soon afterwards a cylinder of acetylene fuel gas exploded, sending flames bursting through the roof.
June Phillips, head of Brookvale school in Runcorn, congratulated pupils and staff on their response. She said: "It was a fire when the children were in school, which is not often the case. But there was no panic and it was a very orderly evacuation.
"We think it was a 13-year-old pupil who actually broke the glass of the fire alarm but at the same time a member of staff was raising the alarm and a support member of staff had gone to the reception to phone the fire brigade. "
The school held regular fire drills and two years ago drew up a 10-point list of rules to ensure children followed procedures, she added.
The cost of the blaze, which destroyed one of the school's two blocks, is put at Pounds 2 million.
A large amount of GCSE coursework, as well as personal belongings, was lost. Discussions are being held with the main examining boards and pupils have been offered stress counselling.
An investigation to establish the cause of the fire was launched by the fire brigade and the Health and Safety Executive.
According to a fire brigade spokeswoman, it started when pupils in the technology workshops were using welding equipment.
The 70 firefighters who tackled the blaze were warned about the acetylene before it exploded.
The spokeswoman added: "The whole school was evacuated within three minutes which was pretty quick work by the teachers. They did very well."
The Fire Prevention Association says the majority of school fires occur out of hours or during holidays. In 1994, the latest year for which figures are available, there were 43 serious fires in educational establishments, 31 were arson attacks. The damage cost almost Pounds 18m.
The general trend is downwards: both the number and cost of school fires has fallen consistently since 1990 when there were 143 major incidents costing a total of Pounds 50m.
The number of school fires as a percentage of all serious fires has also fallen, from 13 to 7 per cent. However, arson attacks are rising - from 61 per cent of all school fires in 1990 to 72 per cent in 1994.