Female students made up 50.3 per cent of entries in biology, chemistry and physics at A-level, whereas boys made up 49.7 per cent of entries, national figures show.
It follows a major push to encourage girls to take up science, technology, engineering and maths (Stem) subjects in school.
An increase in female role models in science, as well as significant effort to tackle stereotypes, are likely to have increased uptake among girls, exam boards and school leaders suggested.
The figures were revealed as tens of thousands of students in England, Wales and Northern Ireland received their A-level results.
The proportion of students awarded an A* or A this summer dropped to its lowest point in 12 years to 25.5 per cent, which was almost 1 per cent less than last year, amid major exam reforms.
Meanwhile, the proportion of students who scored the top grade of A* also fell to 7.8 per cent this year – its lowest level since 2013 – compared to 8 per cent last year.
Exam boards attributed the decline in the top marks to a shift in students’ subject choices towards those which are traditionally considered more difficult – including the sciences.
A growth in the numbers taking A-levels this year could also be behind the trend, they added.
But the overall A* to E pass rate was 97.6 per cent, unchanged on last year, the national figures published by the Joint Council for Qualifications (JCQ) revealed.
Experts had predicted that that the linear structure of the new qualifications would favour boys, but girls outperformed boys at the top grades this year after two years of males doing better.
The proportion of girls who got an A or A* higher was 25.5 per cent, 0.1 percentage points higher than boys (25.4 per cent).
But on A* grades alone, boys performed better, with 8.2 per cent of entries getting the highest result, compared with 7.5 per cent of girls’ entries.
Dr Philip Wright, director general of the JCQ, said the picture shown by the results was “stable”.
He said: “It is particularly encouraging to see the rise in young women being inspired to take science A-levels. For the first time female entries have overtaken male entries in the sciences.”
On Thursday, England’s exam regulator Ofqual announced an investigation into the grading of last summer’s maths A-level – which was the first time the new exam was sat by students.
It is understood there are concerns that grade boundaries set last year may have been too high.
Students who took the A-level in 2018, which was fewer than 2,000, could see their results changed.
The figures released on A-level results day also revealed that Spanish has become the most popular foreign language, with 8,625 entries compared to 8,355 for French.
Meanwhile, the number of entries to political studies and geography rose this year – and a growing interest in climate change, Brexit and US politics could be behind the trend, exam boards said.
But the number of A-level students choosing to study arts subjects and English has continued to fall, prompting concerns about the arts sector being in danger.
Michael Dugher, UK Music CEO said: “This year’s A-level entry numbers reveal a deepening crisis facing music in education that needs urgent action from the government.
“There is yet again a worrying drop in the number of people studying music to A-level, which seriously jeopardises the talent pipeline on which our industry relies.
As the A-level results were published, separate figures revealed that fewer students have been accepted on UK degree courses this year.
The Ucas data shows that 408,960 students, from the UK and overseas, have taken up university places in the UK – down 1 per cent on the same point last year.
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