An expected revival of boys' comparative GCSE fortunes prompted by the replacement of coursework with "controlled assessment" has failed to materialise.
Girls opened up the gap to a record 6.7 percentage points, with 26.5 per cent of entries achieving an A*A compared to 19.8 per cent for boys in the year controlled assessment was introduced in many subjects.
Professor Alan Smithers had said he thought the new assessment method which allows pupils to prepare in advance for a piece of work they write in the classroom under controlled conditions might help redress the gender gap and clip girls' wings.
The Buckingham University academic said conventional coursework played to female strengths.
"It has not been limited in time so in a sense it is a measure of hard work rather than understanding," he said. "But if it is time-limited it is likely to reflect understanding more and therefore you wouldn't expect such a big gap."
But girls also outperformed boys at A*-C overall, and they increased their lead at the higher grades in separate sciences, unlike A-level sciences where boys closed the gap this year.
Association of School and College Leaders general secretary Brian Lightman said: "Even controlled assessment is more suited to the way girls work. Boys tend to respond better to last-minute revision."