Nagaland University, the 13th Central University and the only Central University in Nagaland was established based on the Act of Parliament of India and received the assent of the President of India on 20th October 1989 as THE NAGALAND UNIVERSITY ACT 1989 (No. 35 of 1989) and came into force as notified in THE GAZETTE OF INDIA EXTRAORDINARY PART-II SECTION-1 in October 1989 published by the Ministry of Law and Justice (Legislative Department), New Delhi.

The University came into being on September 6, 1994 having jurisdiction over the entire state of Nagaland. Prior to this, Nagaland had been in the catchment area of North Eastern Hill University (NEHU), with Kohima designated as one of the campuses of NEHU along with SASRD-Medziphema. With the establishment of Nagaland University, the two erstwhile campuses inherited from NEHU as well as the colleges affiliated to it fell within the jurisdiction of Nagaland University. The nascent University had to go through many teething problems initially. The Headquarters of the University, i.e. Lumami, as per the Act could not immediately accommodate the needful so as to start functioning as Headquarters. Hence, for nearly a decade and half Nagaland University had been functioning from Kohima as the interim Headquarters of the University. Meanwhile, the establishment of the academic departments was sanctioned by the Government in the year 1997. All the new departments had to be located at Lumami and started functioning with Kohima still as the interim Headquarters. Constructional activities started earnestly making it fit for academic pursuits at the Headquarters in the best possible way. Upon the completion of new constructions to a reasonable stage, the shifting of interim arrangement at Kohima to Lumami took place in the mid year of 2010.