Chris Whitehead also addressed more than 1,350 pupils at morning assembly wearing the black skirt, which boys are permitted to wear due to a loophole in the policy, the Daily Telegraph reported.
He said that forcing boys at Impington Village College, near Cambridge in eastern England, to wear long trousers during the summer months has a detrimental effect on concentration and their ability to learn.
"In the summer girl students are allowed to wear skirts but boys are not allowed to wear shorts," the schoolboy said.
"We think that this discriminates against boys. I will march in a skirt with other boys waving banners and making a lot of noise.
"I will be wearing the skirt at school all day in protest at the uniform policy and addressing the assembly with the student council, wearing a skirt."
Chris marched to school through the village alongside half a dozen pupils waving banners.
His mother Liz Whitehead, 50, has praised her son for standing up for "what he believes in".
She said: "I am really proud he is brave enough to wear a skirt to school for what he believes in and back him all the way."
Headteacher Robert Campbell said the ban on shorts was imposed two years ago following consultation with parents, pupils and teachers and was "typical" of most schools in the area.
"Chris is a very bright and articulate student and we have got a very strong student council," he said.
"I know he wants to go into politics and has got strong principles," said the headteacher, before joking: "So maybe parliament is not the best place for him."
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