The school is introducing a "trouser uniform" and a "skirt uniform" that can be worn by pupils up to age 16, regardless of their biological gender.
At least one person with gender dysphoria has taken up the option, according to the college.
Head Richard Cairns said the change to its 170-year-old code followed requests from a "small number of families".
"It ties in with my strong personal belief that youngsters should be respected for who they are," he added.
'Welfare and happiness'
"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."
Mr Cairns said whereas most schools gave transgender pupils "personal leeway with uniform" he wanted to "abolish the notion of boys' and girls' schools 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."
Fred Dimbleby, a sixth-form pupil at the college, said the change had support across the school and gave Brighton College a "real sense of unity".
"I think it would be great if all schools took up this idea. Secondary school is such a formative period for people so it's important to encourage people to be who they are and who they want to be."
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