North Halifax Grammar School regularly tops the league tables in Calderdale, West Yorkshire. This year 96 per cent of pupils achieved five GCSE A*-C grades.
Yet it has been judged to add less than average "value" to its pupils' education, with a low-ranking "D" grade - the same as The Ridings School next door.
John Dunford, general secretary of the Secondary Heads Association who campaigned to have the new measure abandoned, said the case exposed it as meaningless and highlighted the anxiety it will cause schools.
The Government has confirmed it will press ahead and publish the "performance indicator" in next month's secondary-school tables, despite widespread criticism. The indicator measures progress between key stage 3 and GCSE results.
Mr Dunford said: "This latest piece of statistical gymnastics from the Government tells parents nothing. It is not a realistic assessment of value-added because it only considers a small part of pupils' school career.
"These schools probably did very well for their children between the ages of 11 and 14 which puts them at a disadvantage under this progress measure.
"Schools are very nervous about their gradings and how it will make them look compared to their neighbours."
The Ridings School, in Halifax, became notorious after an emergency inspection condemned it as a threat to public order in 1996.
Two years on, it has been taken off special measures, but ranks in the bottom 25 per cent of schools in terms of boosting the performance of 14 to 16-year-olds. And now so does North Halifax grammar, a high-performing grant-maintained school with more than three applications for every place.
The Government's new "value-added" measure, called the Performance Indicator, measures improvement between 1996 key stage 3 tests and this year's GCSE results.
Each school is grouped with about 120 others which achieved similar KS3 results in 1996. Progress is compared to the group average and schools are graded A to E.
Graham Maslen, head of North Halifax grammar, believes erratic KS3 marking undermines the new measure. He said: "I have no problem being compared to other schools as long as you compare like with like.
"I resent the fact that all the work we have done is being reduced to one abstract statistic which is completely flawed.
"Our pupils are entered for nine exams and even if they all got A*s this measure would have made it virtually impossible for us to get more than a C."
Anna White, head of The Ridings, also criticised the new indicator. She said: "The performance measure is a fairer method than just looking at five A-C scores but it needs to look at the value schools add from when they join the school at 11 rather than just over the two years before GCSE."