Some 26.1 per cent of A-levels sat by boys were graded an A, compared with 27.9 per cent of exams taken by girls.
The 1.8 percentage point gap is smaller than at any time since 2001 when the examinations system was subjected to a major overhaul.
Under the Curriculum 2000 reforms, AS level exams were introduced in the first year of sixth-form and courses were broken up into a series of six modules that students could re-sit to boost their grades.
Academics said the changes helped girls because they were generally “more conscientious” and benefited from regular assessment. In the years running up to 2000, boys generally gained more A grades.
But under new changes introduced this year, the number of modules has been cut from six to four and exams have been based on more challenging essay-style questions. A new A* grade has also been introduced to pick out the most exceptional candidates.
According to the latest figures, 8.3 per cent of exams taken by girls were A*s, compared with 7.9 per cent of boys’ A-levels. But boys out-performed girls in the more traditional subject areas such as maths and science.
Overall, one in 12 papers were awarded the new A* grade, pushing the total proportion of As up to a record 27 percent.
Prof Alan Smithers, director of the Centre for Education and Employment, based at Buckingham University, said: "In previous years there were six modules and this was really rewarding conscientious application.
“This is something that girls are more likely to do, they are more inclined to apply themselves than boys.
"Boys tend to favour end of course examinations."
Boys scored more A* grades in chemistry, communication studies, computing, maths and further maths.
In English, 7.5 per cent of boys' entries were awarded the top grade, compared to 7.3 per cent of girls' entries. Boys also did better in some languages, such as Irish and Spanish.
Prof Smithers added: "I think boys, by and large, find numbers easier to handle than words. It can be traced back to the early years when girls are ahead in terms of using words and reading, and boys are ahead in numerical subjects."
According to the latest figures, the gap in the overall A-level pass rate has also remained at its narrowest point since the mid-90s.
Some 97 per cent of A-levels taken by boys were graded A* to E, compared with 98.1 per cent of girls. This was the same as last year but smaller than the 1.3 percentage point gap recorded in 1996.
Universities minister David Willetts today acknowledged that even students gaining a clean sweep of top grades may still miss out on their choice of degree course. He said he was "sorry" for those who failed to secure their prefered place.
Speaking at the headquarters of Ucas in Cheltenham, Gloucestershire, Mr Willetts, Minister for Universities and Science, said: ''There are more places at university than ever before, and in fact, at this moment, more prospective students have now got a definite firm place at university than at this point last year.
''But sadly there will be people who have applied to university and don't get a place.
''It has always been a competitive process but for them we've got the widest possible range of alternative options, including, of course, studying at Open University, studying at an FE college, going into work with an apprenticeship. All those options are available as well.
''I think it is great that young people aim high, but it is competitive and sadly not every person who applies will get a place.''
Asked what he would say to students left without a place at university at the end of the clearing process, he said: ''I would say to them, we have done our best, there are more university places than ever before. I am sorry that they haven't got a place.
''And now, they have got a big decision to take. They can think about how they can strengthen their CV and reapply next year with something that might improve their chances."
--By Graeme Paton,19 Aug 2010