Brighton College has scrapped its uniform code in order to accommodate transgender pupils.
The independent school is introducing trouser and skirt uniforms, which can be worn by pupils up to age 16, regardless of their gender.
Headteacher Richard Cairns said he had changed the 170-year-old rules after requests from a "small number" of families," the BBC reported.
"It ties in with my strong personal belief that youngsters should be respected for who they are," he said.
"If some boys and girls are happier identifying with a different gender from that in which they were born, then my job is to make sure that we accommodate that.
"My only interest as headmaster is their welfare and happiness."
Cairns added he wanted to abolish the notion of boys' and girls' school uniform altogether.
"Traditional uniform will be worn but the type of uniform will be a matter for the individual boy or girl, always assuming parental support," he added.
In 2012, it emerged a headmaster had tried to ban a transgender schoolboy from sitting an exam dressed in girls' uniform. Ashlyn Parram, 16, wore girl's tights, a skirt and blazer to her first GCSE exam but was told she could not sit the paper, because she was not in correct uniform.
Last year, boarding schools were told to adopt gender neutral uniform policies in order to avoid discrimination against lesbian, gay, bisexual and transgender (LGBT) pupils.