A three-year study of pupils taking physics shows girls scoring an average of one-fifth of a grade less than boys.
The findings come as the latest GCSE statistics show an increase in the number of pupils taking combined sciences. Sir Ron Dearing and the School Curriculum and Assessment Authority have both warned that students on combined courses could be at a disadvantage when they move on to A-level.
The study of pupil performance in single-subject sciences was conducted by Ann Benson, a science education lecturer at the University of Bristol. Her results will be presented to the European Science Education Research Association next month.
She will tell the conference that girls' physics results could be suffering partly because of the way their work is assessed. "I think it's more than social or cultural factors," she said this week.
Girls now match or do better than boys in every other subject at GCSE, scoring one-fifth of a grade better overall, according to Mrs Benson. But their failure in physics is causing alarm as they continue to reject the subject at A-level - Government figures show there were just 6,211 female candidates in 199596 compared with 23,308 males. They remain absent from engineering-based degree courses.
Catherine Wilson, education manager for schools and colleges with the Institute of Physics, said: "If you can show girls they are getting good results, then they will begin to believe in themselves a lot more. They become more likely to carry on with physics."
Previous attempts to show the gender divide have been dismissed with the argument that the single-subject sciences are taken mostly in independent or selective schools. But Mrs Benson's research is based mainly on pupils from maintained, co-educational comprehensives.
Combined GCSE science courses have been credited with keeping girls involved with science to the age of 16 and beyond.