"Laddish culture" has been blamed for the disparity in results between the sexes, which has seen girls consistently performing better in recent years.
According to figures from the Joint Council for General Qualifications - which compiles figures for all exam boards in Wales - 59.7% of all entries passed the exams with grade C or above.
Of those, 64.2% of girls passed at C or above compared with 55% of boys.
Boys still do better in science subjects, and Latin is one of a few areas of male dominance.
In the Welsh first language exams, 67.1% of boys passed with grades A* to C compared with 82.5% of girls.
David Hart, the National Association of Head Teachers general secretary, said: "This year's results clearly demonstrate a good performance by many students but the boys are dragging down the results.
"There is not a cat in hell's chance of significantly reducing the 40% of results that are below grade C unless the boys raise their game.
"There are no quick fix solutions to the problems caused by the anti-learning laddish culture.
"But solutions will have to be found if the government's performance targets are to be met by the next election."
Praise
Education Minister Jane Davidson praised the work done by pupils, teachers and parents in the run-up to exams.
She said: "These results show that we are maintaining the high standards achieved in Wales and they compare very favourably with the national picture.
"A pass rate of 98% is excellent and I should like to congratulate pupils and teachers throughout Wales on their success.
"These results set alongside last week's A-level achievement show clearly that Wales is a learning country where all pupils, students and young people have the opportunity to give their best and achieve their best."
Teenage singer Charlotte Church was amongst those celebrating as she passed all seven of the GCSE exams that she sat.
She said she was "absolutely delighted" with her three A*s (including music) and four As.
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