Yesodey Hatorah senior girls', a comprehensive which serves the Charedi community in Hackney, east London, is England's leading performer on value-added results.
Nationally, the tables showed English results falling by a percentage point to 73 per cent achieving the expected level. Maths scores rose by three points to 77 per cent, while science was up two points to 72 per cent.
Some 81 per cent of Yasodey Hatorah's pupils achieved level five in English; 96 per cent in maths; and 92 per cent in science. More than eighty per cent achieved level six in maths and science, while in English, the figure was 52 per cent.
This is comfortably above the national average, even though girls arrive at the school with average key stage 2 results in English and only slightly above national figures in maths and science.
The results come after the school, which was set up privately in 1942 but joined the state sector in 2005, received an outstanding Ofsted report last September.
Rabbi Abraham Pinter, the principal, put its success down to the sense of responsiblity the school instils. It insists that everyone sits English, maths, science, languages, history and geography GCSEs.
The school, which has only 233 pupils, has computers and somtimes features video clips in lessons. But members of the community it serves do not watch TV or use the internet at home. Rabbi Pinter said this might be an advantage: "The popular media does waste a lot of pupils' time," he said.
Yesodey Hatorah was one of only 14 comprehensives to feature in the top 100 value-added schools, a ranking that compares pupils' KS3 results with their KS2 scores. Grammar schools dominated both this list and the "raw score"
England's three top-performing secondaries were all girls' grammars: St Michael's RC in Finchley, London; Wolverhampton girls' high; and Kendrick girls' grammar in Reading. All pupils from these three achieved at least level 6 in English, maths and science.
Critics say the value-added measure favours middle-class schools since it is harder for disadvantaged areas to make progress.
A new measure is to be introduced next year that will assess pupils' KS3 and KS2 scores alongside other factors, including poverty, ethnicity and gender.
Thomas Telford school, the city technology college that topped national GCSE league tables, bolstered its reputation by finishing as England's top-performing comprehensive in the raw score tables.
Some 99 per cent of its pupils gained level 5 or above in English, maths and science, with at least three-quarters reaching level 6 in each of the tested subjects. It finished 125th overall.
The rankings brought mixed news for academies. All but one of the 12 that had results from 2005 and 2006 improved their scores. The Bexley Business academy was the third most improved school, having doubled the proportion of pupils achieving the expected level in English, maths and science since 2003. Greig City academy, London, was 57th most improved. But only six of the 25 academies that had results for 2006 registered above-average value-added performances. The most improved school overall was The Lafford high school in Billinghay, Lincolnshire, which is thriving after going into partnership with neighbouring St George's college, in Sleaford.
The Ridings school in Halifax, which is expected to go back into special measures next week, came 10th from bottom in the table.
Top Ten of the best
Top six KS3 "raw scores"
1 St Michael's RC grammar, Finchley, London: 300300
1 Wolverhampton girls': 300300
1 Kendrick girls' grammar, Reading: 300300
4 Ermysted's grammar, Skipton, North Yorkshire: 300299
4 Lancaster Royal grammar, Lancaster: 300299
4 Adams' grammar, Newport, Shropshire: 300299
The first quoted figure is the total of the percentages of pupils achieving level 5 in English, maths and science. The second figure is the total doing so at level 6.
Top five KS3 "value-added"
1 Yesodey Hatorah senior girls', Hackney, London: 105.2
2 Queen Elizabeth's, Barnet: 104.2
3 Sutton grammar for boys, Sutton: 104.1
4 Reading school, Reading: 104
5 The Five Islands school, Isles of Scilly: 103.9
Number quoted is the school's value-added score. Every point above 100 represents one extra term's progress, on average, for each pupil compared with what would be expected given their KS2 results.