Kate Bailey was recruited to head John Keble Church of England school in Harlesden, west London, at the beginning of 2001, on a salary of pound;61,719. Her replacement starting in January 2003, has been offered pound;62,406 including London weighting.
The inner-city school was already failing when Mrs Bailey took over 18 months ago.
Inspectors put the school in special measures in May 2000. They set out five key tasks for the school's leaders: raise standards, improve teaching, give a clear educational direction for the school, ensure the curriculum is sufficiently balanced and continue to work with parents to ensure punctuality.
Their report pointed out there was a high proportion of children entitled to free school meals, 42 per cent, while even more (44 per cent) had special educational needs.
The school roll has dropped from 469 in 1999 to 455 in 2001.
National curriculum test results in English rose slightly after a dip in 2000 with 74 per cent of 11-year-olds achieving the expected level 4 in English in 2001.
But in maths, just 52 per cent reached the required standard, a drop from 63 per cent in 1999.
Mrs Bailey issued a statement through Brent Council. She said: "After careful consideration I am resigning from my position as headteacher of John Keble school. I have decided to accept the opportunity to make a career move and to take a new professional challenge.
"I appreciate the support shown to me by staff, parents and governors over the last year and a half and wish the pupils and school well for the future."
The authority's advertisement for the post she vacates says that the new head should have the ability to manage with sensitivity; the ability to develop and nurture a successful team, high expectations; a commitment to developing the potential of all children; and a firm commitment to the school's ethos and Christian values.
The applicant should also have substantial leadership experience.