The 500 schools also have a better ethos, according to the study, and pupils attain a higher level of maturity and responsibility for their work by transferring to secondary schools a year later.
The findings will be welcomed by advocates of the middle-school system, which is being squeezed out by local reorganisations.
The study, based on data from the Office for Standards in Education, was carried out by researchers from Keele University on behalf of the National Middle Schools Forum. The results were revealed at the organisation's annual conference in Suffolk, sponsored by The TES, this week.
They found that middle schools offered good value for money, contrary to the popular belief that they are more expensive to run.
However, in terms of overall attainment of pupils across all subjects the study was inconclusive. Research fellow, Michael Johnson, said the OFSTED information showed "no huge distinctions" in standards between children who had transferred to secondaries from primary and middle schools.
Roger Loose, Suffolk's senior adviser for the curriculum and assessment, said the results supported the county's own experience. Suffolk is one of few local authorities which still has a primary and middle school system.
Mr Loose said teachers in middle schools had to plan the progress of youngsters and "make greater efforts to co-operate with secondary schools" to bridge the gap which splits key stage 3.
Peter Hunt, the forum's vice-chairman, said one of the aims of the conference was to promote middle schools at a time when they are in decline nationally.
He said: "Middle schools are being closed apparently for financial rather than educational reasons. However, it has been shown how effective they are in terms of teaching and learning."
Mr Hunt, who is head of Bacton middle school, near Stowmarket, added:
"Those of us in this system know what a wonderful experience it is to work with children in a wide-ranging age group who are at their most enthusiastic."