Arjun, a student of MGM Model School in Varkala, hung himself at his home on Tuesday.
His relatives have now alleged that he was mentally harassed by the school's teachers and vice-principal.
The school authorities had reported Arjun for malpractice during an exam recently.
It is understood that they had called for his parents and threatened to suspend him and report the matter to the CBSE.
However, the school authorities have denied the charges and said they called for the parents as any school would do in the situation.
Jishnu Pranoy, a B-tech student of Nehru College of Engineering in Thrissur, had committed suicide around two months ago, allegedly due to abuse and harassment from the college authorities.