The institute is managed by a Board of Management, comprising representatives of MHRD, the eight beneficiary states of the North Eastern region, AICTE and educationists. The state governor of Arunachal Pradesh is the "de facto" head of the highest body, NERIST Society, which consists of education ministers of all North Eastern States. The Board of Management is headed by the director of Indian Institute of Technology Guwahati, Gautam Baruah. The board appoints a well-known academic, generally from north east India, as director of NERIST.