The study by academics at York university casts doubt on the government policy of encouraging schools without sixth forms to set one up.
The study commissioned by the Department for Education and Skills, was based on statistics from 2,928 of England's 2,997 secondaries. It found lower value-added scores in the 1,674 schools with sixth forms compared to the 1,254 without. Researchers used figures comparing the GCSE performance of pupils in 20034 to their key stage 3 national test results.
Using a statistical formula, they removed other possible factors, including the number of teachers, support staff, and clerical staff per pupil; money spent on resources per child; and the numbers of special educational needs pupils, children eligible for free school meals and those with English as an additional language.
They found that once these were stripped out, the absence of a sixth form was found to add an average of just over a third of a GCSE grade per pupil to a school's value-added score.
Martin Ward, deputy general secretary of the Association of School and College Leaders, said: "Some schools may have a tendency to look forward to A-levels rather than squeezing the last possible grade out of their pupils at GCSE."
Another reason for the difference could be that schools with small sixth forms were using money ear-marked for 11 to 16-year-olds to subsidise post-16 funding, he said.
Sue Witham, from the Sixth Form Colleges' Forum, said: "This research shows that having 11-16 schools and separate sixth-form and further education colleges is one of the best structures, allowing different institutions to concentrate on their own part of the system."
The researcher, also found that secondaries with large proportions of pupils with English as an additional language produced better value-added GCSE results.
Schools that spent more on resources were more likely to achieve better value-added scores, says the study. However, higher staff-to-pupil ratios appeared to make no difference to results.
This could be because good results in better staffed schools were cancelled out statistically by the extra staffing that struggling schools received.
Analysis of Secondary School Efficiency, by Professor Peter C Smith and Dr Andrew Street, can be found at www.dfes.gov.ukresearchunder published projects