Heads leaders' fear the most disadvantaged secondaries will suffer financially when the National Challenge scheme ends on Thursday.
The Government has already introduced a new strategy for "underperforming schools" which it says will be fairer by taking pupil progress into account alongside raw exam results.
It will also continue some of the key concepts used in the National, London, Greater Manchester and Black Country Challenges, such as supporting schools by allocating them external advisers.
But Malcolm Trobe, Association of School and College Leaders policy director, said: "The Challenges ensured there was some targeted support in areas of the greatest need but we have significant concerns about whether this will carry on."
Mr Trobe said that although money to support such schools was supposed to have gone into the general schools funding pot, it was "difficult to see if in reality that has happened". He also said local authorities now lack the funding to work with schools "in challenging circumstances".
The #163;400 million National Challenge got off to a controversial start when it was launched by the then Labour government in 2008. Ministers used the word "failure" when discussing 638 secondaries with low results and publicly threatened them with closure (see box).
Those who led the National Challenge say that although some headteachers might still be resentful, others ended up being reluctant to leave the scheme and the support offered.
Mr Trobe said: "It wasn't launched in the best possible way but overall the National Challenge had a positive impact."
He said there was "no doubt whatsoever" that the London Challenge - which inspired the national scheme - had made a "significant" difference. There was also evidence that the Greater Manchester Challenge, launched in 2008 with the Black Country Challenge, had worked.
Professor Mel Ainscow, Greater Manchester Challenge chief adviser, said: "We hope the concepts don't disappear. Schools here have become like laboratories for ideas.
"We have brokered a new relationship between teachers; the potential of this is phenomenal. We are optimistic that the best of what we have achieved can be sustained."
A Department for Education spokesperson said: "The new schools commissioner Dr Elizabeth Sidwell is already working with underperforming schools to develop robust improvement plans and to challenge poor performance.
"We're bringing in much fairer floor standards for schools. Ministers have been clear that previous performance targets were far too crude and that schools with challenging intakes often felt stigmatised."
London Challenge, pages 34-35
Did it work?
'It was a travesty'
Waverley School in Small Heath, Birmingham, was among one of the first schools included in the National Challenge. It was still in the programme two years later, despite clearing the Government's GCSE target, being rated "outstanding" by Ofsted and having one of its heads appointed to advise schools in the Black Country Challenge.
Waverley's assistant head Ian Healey said: "The National Challenge was ridiculously flawed because it judged schools by one yardstick without any context. It was a travesty." But he said it had created "strength in adversity" among staff, driving improvements that led to the Specialist Schools and Academies Trust identifying Waverley as having the best added-value results in the country last week.
Mr Healey also said the external advice provided by the National Challenge was useful. But he added: "Any help we received was outweighed by the stigma attached to the programme."