Sally Carr, 50, is taking early retirement from Rams Episcopal primary in Hackney, north London, only two terms after arriving at the school, which has been in special measures for the past five years.
She chose to leave after plans were announced to relaunch the school this September under the Government's controversial Fresh Start programme.
The Fresh Start proposals followed the the school's unsuccessful partnership with private consultants, the Centre for British Teachers (CfBT).
Ms Carr told The TES that the stress of Fresh Start, under which schools are re-opened with a new name and often new staff, risked leaving her a "nervous wreck". She said only two of the school's 12 staff had been guaranteed jobs when it re-opens in September.
She said: "It was my decision not to apply for the post that went with the Fresh Start school - I can't see how any one person can run down one school and then set up another.
"My contract would have finished in July. But it's been an incredibly stressful time here. If you are trying to move the school forward as well as trying to deal with the personnel issues that Fresh Start creates, it is very difficult.
"It was not worth turning myself into a nervous wreck by staying on another term."
Ms Carr took over last September after CfBT's contract ceased. CfBT has since claimed the local authority and governing body failed to back its improvement plans.
Her decision to quit is the latest in a string of setbacks for the Church of England primary.
Th problems associated with the Fresh Start scheme have been further highlighted in Sheffield,where the city council is worried it will not be able to attract experienced staff to apply for jobs at schools re-opened under the scheme.
Now, it has pledged that the jobs of senior teachers who join the city's latest Fresh Start will be secure, even if the project fails and the school has to close.
Staff appointed to the 12 senior management posts at the school replacing the failing Herries school in David Blunkett's constituency, will get a guarantee from the city council of comparable employment elsewhere if the project does not work.
The Government has insisted it will shut schools where results over three years are poor. Last year only 4 per cent of candidates at the Herries school achieved five or more higher-grade (A*-C) GCSEs - well below the 15 per cent target that has been set by ministers.
The Herries will re-open in September under new headteacher, John Leam. Unlike his senior staff Mr Leam, who has been recruited from Isaac Newton school in Hull, will not get a job guarantee.
All teachers at the school are to get training and support co-ordinated by the Leadership Centre, the professional development centre for teachers and managers opened at Sheffield Hallam University last year.
Jonathan Crossley-Holland, Sheffield's director of education, said: "We have been looking at ways to attract senior managers. The job guarantee removes the risk involved for the individual should the school fail."
A similar job guarantee is likely to be offered to applicants for senior teacher posts at the city's other failing school, Hinde House.