Townsend Church of England school, St Albans, was the only one in Hertfordshire to win a Government Charter Mark this year.
However, headteacher Andrew Wellbeloved believes its future is being undermined by its position at the bottom of its area's tables.
He said: "There is this huge conflict between our table position and winning this award. What do these league tables mean?" Last year, 36 per cent of Townsend's pupils achieved five GCSE grades A-C, putting it bottom of the 12 secondary schools in St Albans and Harpenden.
Mr Wellbeloved said: "The league tables become a self-fulfilling prophesy. They affect the recruitment of pupils and damage our finances. Although this award shows we are doing well, it is very difficult to break out of the cycle."
Townsend school's close relationships with parents and pupils were judged to be "particularly strong" and it was also commended for its partnership with the nearby Heathlands school for the deaf, from which it draws 40 of its 831 pupils.
Only 508 organisations have been selected from 30,745 nominations to win Charter Marks in 1999. Seventy-six of the winners are from schools, colleges and universities, an increase on last year.
The more unusual winners include the Kingston-upon-Hull governors team which recruits, trains and supports school governing bodies. The team provides a free clerking service and consults governors on developments in the authority.
To achieve the standard, applicants had to pass stiff tests in nine key areas of public service, demonstrating tough performance standards, providing excellent value for taxpayers' money, and showing year-on-year improvement in standards.
Another star of this year's Charter Mark awards was St Mary's College, Creggan, Derry.
Principal Geraldine Keegan was invited to meet ministers after the college become one of only 18 organisations to achieve the accolade for a third time.
Its trophy cabinet also includes Investors in People status, School Curriculum awards, Northern Ireland Quality awards, and a special award for lifelong learning.
HOW THE MARK IS WON
The Charter Mark is awarded against a range of criteria including:
* information and openness
* consultation and choice
* courtesy and helpfulness
* value for money
* user satisfaction
* improvements in service quality
* planned improvements
* putting things right