The police have registered a case of murder after the boy's family alleged so.
"We reached here after we got information about a dead body being found in the madrasa. We have called the Forensic Science Laboratory (FSL) team here and are investigating the incident," Assistant Superintendent of Police (ASP) Usha Kunda was quoted as saying by news agency ANI.
The victim had reportedly been studying in the madrasa for a year.
'This is Murder': Boy's Kin
Suspecting that he was murdered, the boy's kin said, "I was told that my nephew had left the madrasa (on Saturday) but did not reach home. We searched for him but couldn’t find him anywhere. This is murder."
Maulana Zakir, the director of the Islamic Madrasa, Dargah Shah Chaukha, said that the boy was present during the evening prayers but went missing when the attendance was being taken.
He also said that the boy's body was found in one of the rooms of the mosque.
"The 11-year-old was studying here for nearly one year. He studied Urdu and Arabic here. On Saturday evening, he was present during the prayers. But when the attendance was taken at 7 pm, he was missing," Zakir said.
He also added that when he wasn't found, his family was informed, and several people also searched for him in the nearby villages and mosques.
The family has demanded that strict action be taken against the accused.
Congress Urges Probe Into Demolitions of Madrasas in Assam
This comes amid a raging controversy concerning madrasas, especially in Assam, where several of them have been demolished in recent weeks.
On 29 August, the Himanta Biswa Sarma-led government demolished a madrasa in the state's Barpeta district, alleging that it was used for "anti-national activities."
They alleged that the people who managed the madrasa were connected to the dreaded terrorist outfit Al Qaeda.
Meanwhile, the Assam Congress wrote to the National Commission for Minorities (NCM), urging them to launch a probe into the demolition of a madrasa in Bongaigaon.
In a letter to NCM Chairperson Iqbal Singh Lalpura, Congress MP Abdul Khaleque, and several MLAs, alleged that the madrasa's demolition was "in blatant disregard to the rule of law."
Giving justifications for the demolition, CM Sarma had said that the madrasa was razed under the Unlawful Activities (Prevention) Act and the Disaster Management Act as it did not have permission from the local panchayat or the district administration to be built on that specific plot of land.
Sarma alleged that the madrasa's mufti was an important financial conduit for Ansar ul Islam, a militant Islamic group, and that money was deposited in his account often.
(With inputs from ANI.)