Tusshar, 16, was found unconscious by some students in his school bathroom and was taken to a hospital on Thursday.
He was later referred to the GTB Hospital where he was declared brought dead.
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.
CCTV footage later revealed that he had a fight with some students near the washroom.
On the basis of a complaint by the boy's family, a case was registered.
Three of the students with whom he had a fight have been apprehended, said a senior police officer, adding that they were minors.
One more student is on the run.
Family members of the deceased alleged that he was thrashed by the students.
The post-mortem of the body was yet be conducted by a medical board till reports last came in.
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.
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