Some schools would have performed much worse than official league tables show if "churn rates" had been taken into account, it has been claimed.
Data from Education DataLab shows about 20,000 secondary pupils left before they sat their GCSE exams.
If the students had remained, some schools would not have scored as highly on the official league tables.
Of the 100 schools in England which would have seen the biggest shift, 62 were in London.
The figures are from 2,901 state-funded secondary schools in England across four years.
Education Datalab, an independent research group, recalibrated the results according to how long each pupil spent in each school.
Each pupil should spend 15 terms in secondary education. For example, if a pupil spent six terms in one school, then that school would receive 40% of the results, while the other 60%.
Currently, league tables are worked out from how many children were on-roll in January of their final year.
Children may leave school because of being managed out, expulsions or moving house. They are also more likely to be from poorer backgrounds or have special educational needs.
'Boost league table'
The figures show Harris Academy Greenwich would have seen the biggest impact on its league table position. One year it would have seen its GCSE pass rates for grades A-C drop by 15%.
In the last four years 611 pupils completed their secondary education at the school, while 217 left before the January of their final year.
Nine out of the bottom 100 were also Harris Academies.
A Harris Federation spokesperson said many of its schools joined the federation because they were failing and had a high proportion of pupils considered to be disadvantaged.
"London - which is where all of our schools are located - has high pupil mobility. It is no surprise that this would be even higher in recently failing schools with very large catchment areas and in areas of disadvantage," the spokesperson added.
But Philip Nye from Education Datalab said there were some weaknesses in the league table system and that it could be improved by making schools accountable for all children.
"We do think in a minority of cases there might be some head teachers who are using pupil moves to boost their league table moves," he added.
A Department for Education spokesperson said exclusions could only be issued on disciplinary grounds and that it was introducing stronger measures to ensure mainstream schools continue to be accountable for the progress of pupils they place in alternative provision.
It has not yet commented on how the school league tables were worked out.