Tusshar (16) was found unconscious by some students in the bathroom and was taken to a hospital. He was later referred to the GTB Hospital where he was declared brought dead, they said.
Though the school administration claimed that he was suffering loose motions, the boy's family alleged that he had a fight with some students and was thrashed, police said.
However, the police said that no injury marks were found on the boy's body.
Police are questioning his classmates and the students who had found him in an unconscious state in the bathroom.
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Tusshar is a resident of Karawal Nagar.
The family also alleged that school authorities were trying to shield the students he had a fight with.
Local residents along with the boy's family members staged a protest at the Karawal Nagar Chowk and demanded a probe into the matter.
Karawal Nagar MLA Kapil Mishra said that he is monitoring the situation and is in touch with the police and hospital authorities.