From this autumn secondary schools will be scored on their "value-added" scores - how far their pupils improved between the ages of 14 and 16.
Heads and governors have long complained that the league tables are unfair because they only include straight results. The tables, published every autumn, have ignored schools' social circumstances and the nature of their pupil intake.
But the new measure, announced by the Government this week, will draw comparisons between their results at key stage 3 and the GCSE results two years later.
This age 14-16 analysis is less complete than a comparison from age 11-16, but will still be an indication of how individual schools are performing. It is the first time that any value-added element has been included in the league tables.
Unions and academics welcomed the new information but remain critical of the league tables.
"We think this is a shift in the right direction," said John Bangs from the National Union of Teachers. "Value-added scores are important but league tables still inflict injustice on the achievement of individual schools."
Professor Harvey Goldstein, a statistician from London University's Institute of Education, gave the move "one cheer". The exercise is helpful to individual schools, he said, but national league tables remain statistically invalid.
"The analysis is quite a useful thing to do. But you cannot produce league tables on that basis. Most schools can't be statistically separated from one another."
Announcing the development, schools minister Estelle Morris said: "We want parents to be able to see not only how their child's school has performed this year but also the progress that it has made in improving the performance of all its pupils."
Next year's tables will also include a new column giving average point scores for GCSEs and GNVQs. This should emphasise the spread of achievement rather than just among grades A*-C at GCSE.
This was praised by the NUT: "We welcome any move to recognise that every child's achievement must be valued."