Brendan Farrelly, principal of the all-girls Craigholme School, in Glasgow, said self-confidence and the freedom to choose school subjects without gender stereotyping were the most important aspects in tackling the issue.
His comments come just weeks after universities and colleges were told to increase the number of women on courses traditionally dominated by men.
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The Scottish Government said "gender segregation" in subjects such as physics, chemistry, engineering and computer science had to be tackled.
Recent figures show 65 per cent of students studying science and engineering courses in Scotland are men, while 80 per cent of those taking computer science are also male.
Mr Farrelly said: "Single-sex education gives female pupils the space to develop as individuals. There is less expectation of gender norms and they are encouraged to look at every career and every level of that career and that means there is no thought that they should not be doing science."
Mr Farrelly joins Craigholme after spending five years as director of studies at Glasgow Academy. Before that he was assistant rector at Wellington School, in Ayr.