The boys from Exeter's ISCA Academy have been told they will be allowed to wear shorts from next year.
The school said the change to the uniform policy was being brought into account for summers getting hotter in the UK but it could not allow an immediate change because it "would put undue pressure on some of our families".
"Shorts are not currently part of our school uniform for boys. Contrary to news reports, we have not banned shorts; shorts are simply not part of our school uniform," the school said in a statement.
The school also clarified that none of the boys who wore skirts in protest have been "penalised".
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"In the meantime, our summer uniform allows students not to wear their jumper or blazer.Also, recognising the recent temperatures, students have also been allowed not to wear ties, to have the top button on their shirts undone, and to wear their shirts untucked if they are feeling very hot," the school said.
The UK has had some of its hottest days this week, leading to the boys requesting permission to wear shorts to classes but were told it was not possible as it went against the school's uniform policy.
Claire Lambeth, the mother of one of the boys who began the protest, said she was proud of him.
"Ryan came up with the idea of wearing a skirt, so that evening we borrowed one. He wore it the next day - as did other boys...I think it was a great idea," she said.
The GMB union has said it will tell all porters who are among its members to wear dresses if he was not reinstated.
"What we're hoping to do is get round the table and get Michael back to work, failing that, the chief executive of Watford General Hospital, [is] going to see her porters wearing dresses. We're going to put out a message to porters [to start] wearing dresses and start wearing skirts," said GMB official Mick Dooley.
When he said he "could not promise" not to roll them back up, he was sent home.