Malcolm Walker, a history teacher at the Headlands school in Swindon, now faces disciplinary action for criticising the management regime brought in to rescue the struggling secondary.
In a letter to 28 14-year-olds, he said: "I do not agree with the way staff and pupils have been treated since the new management took over. I think the permanent teachers have been treated without respect and students have been neglected (denied a proper education)."
More than 100 youngsters walked out last Monday, and many refused to return to lessons.
Staff closed the school later that day and only two of the five year groups were told to come in on Tuesday. The 880-pupil school said the action had to be taken because feelings were running high.
Education officials said they hoped Headlands would be functioning normally again by Thursday, as The TES was going to press.
Headlands was placed in special measures in October 2002.
Last September, John Wells, the headteacher resigned after three years in the job, despite overseeing improved GCSE results.
Last year, just 18 per cent of pupils achieved five or more A* to C grades at GCSE, compared with a national average of almost 53 per cent.
However, there has been a steady improvement in the past three years. In 2000, just 11 per cent of students achieved five or more top grade GCSEs, rising to 14 per cent in 2001 and 16 per cent in 2002.
David Williams, head of nearby Kingsdown school, is at present executive head. Mr Walker's actions will be investigated by Graham Black, Headlands'
Mr Walker told pupils in his letter that he was leaving at the end of term for reasons he could not disclose.
The school refused to comment but a spokeswoman for the local authority said: "Swindon council is aware that a member of staff at Headlands school has independently issued a letter to pupils.
"It is disappointing that the individual did not choose to use the internal communication channels available to express his views.
"This is now a procedural matter for the school and local authority to resolve with the member of staff."
But some pupils said they were upset at Mr Walker's departure because he cared and had inspired them to work hard.
Others said they were concerned about the number of supply teachers at the school.
One 15-year-old girl said: "I am really worried about my grades.
"In Years 7, 8 and 9 I was getting really high grades. Now in Year 10 they have dropped off because of the different teachers I have had."