Levi Keat, 15, donned heavy eyeliner, mascara, foundation, lipstick and blusher, in a subversive take on the #Nomakeupselfie pictures, which girls were posting on Facebook to raise money for Cancer Research UK.
He wanted to raise money for the charity in support of his cousin who is currently undergoing chemotherapy for Non Hodgkin's Lymphoma.
So, he uploaded a selfie showing his made up face on to his Facebook page and asked people to donate to the charity. But when Levi arrived at St John Fisher Catholic School in Chatham, a teacher inspecting uniform at the school gates took him to one side and told him to take the make-up off.
Levi ignored the warning and turned up at his maths lesson still wearing the make-up. There the teacher removed him from the class and told him that unless he removed the make-up, he would be excluded for the rest of the day and possibly longer.
"I couldn't really see a problem," Levi told Kent Online. "I'd seen all these girls going make-up free at school and posting pictures to raise money.
"I thought it was a nice idea and it got me thinking. I had my normal uniform on, it was only my face that was made up."
When Levi told his mother, Carmel Keat, 46, about the school's reaction to his fund raising attempt she was shocked.
"He was so downcast when he told me what had happened," she said. "He had shown a bit of initiative and felt left out as all the girls were doing their make-up free pictures. Most girls in his class wear more make-up than that on a normal day.
"He's an extrovert and always has these bright ideas. To threaten to send him home because of it and take him out of his lessons was way over the top."
Kent Online report that the school has not yet responded to requests for comment.