The beginning of North Eastern Regional Institute of Science and Technology was with a 1979 proposal by the Government of Arunachal Pradesh to establish a science and technology institute with the aim of providing education at various levels in a modular manner. A report, prepared by a team of professors from the Indian Institute of Management, Ahmedabad in 1981–82, was submitted to the North Eastern Council (NEC) which approved it, paving the way to the registering of the society for the institute on 11 January 1983. NEC set up a working group headed by Amitabha Bhattacharya of Jadavpur University, which submitted a project report and a work plan on October 1983. The report was approved by the Ministry of Education in December that year, though final approval from the Ministry of Education was on a letter dated 12 September 1985.
The foundation stone of the institute was set on 4 March 1984 by then President of India, Giani Zail Singh. The institute started operating in 1986 with six base modules. Six diploma modules started in 1988 and by 1990 seven degree modules were added. The institute was initially funded by NEC until, on April 1994, it came directly under the full funding and control of the Ministry of Human Resource Development (MHRD). In May 2005 it was granted deemed university status. NERIST gained approval for Post-Graduate programme from AICTE and MHRD in the year 1996, and the latter was successfully implemented by 2006.
The First Convocation of North Eastern Regional Institute of Science and Technology, marking the Silver Jubilee celebration since the establishment of the institute, was held on 1 April 2009 in the honourable presence of the President of India Pratibha Patil. The Second Convocation was graced by the presence of former President of India Dr. A. P. J. Abdul Kalam held in August 2010. Besides the then Director of NERIST, Dr. Joram Begi, the State Governor of Arunachal Pradesh and president of NERIST Society, J. J. Singh and the Director of IIT Guwahati and Chairperson of NERIST Board of Management, Prof. Gautam Baruah were among the other dignitaries who had attended the occasion.