The establishment of the South Eastern University of Sri Lanka and its predecessor, the South Eastern University College of Sri Lanka, no doubt fulfilled the long felt needs of the people of the South eastern region. The birth of the South Eastern University of Sri Lanka also coincided with more positive thinking and policy of the Government to broad - base University education further, by extending it to periphery and less developed regions in the country such as the South Eastern region. But it was due to certain special and unfortunate circumstances in the country caused by the on - going militancy at that time and civil unrest in the North and East of the country, which actually hastened its establishment. When the militancy and civil strife in the North forced out the Muslim staff and students of the University of Jaffna, ad-hoc arrangements were made to accommodate them mainly at the Eastern University at Vantharumulai in Batticaloa district. But owing to deteriorating communal harmony between the Tamils and Muslims and several unfortunate incidents, which took place in that region, the Muslim staff and students were compelled to leave the Eastern University too, with their studies abruptly interrupted. This problem promptly took up to the notice of the Government to find a lasting solution. The government, which was already keen to expand university education to the less developed region, recognized the need for immediate relief.
The South Eastern University of Sri Lanka commenced its academic programmes under two Faculties, namely the Faculty of Arts & Culture and the Management and Commerce at Addalaichenai, sharing the premises of the Government Teachers' Training College while the construction work of its permanent seat at Oluvil where 220 acres of land has been acquired , was in progress.
In 1997, the Faculty of Applied sciences was established at Sammanthurai with first batch of students for the Academic Year 1997/98 consisting of 30 students for the B.Sc programme in Bio Science and 10 students for Physical Science. In May 1998, Faculty of Arts & Culture and Management & Commerce main University Library and all administrative offices were shifted from Addalaichenai to Oluvil and the Centre for Extension studies of the University remained at Addalaichenai.
In October 2005, the Faculty of Islamic Studies and Arabic Language was established with first batch of 50 students for the Academic Year 2005/2006 then another batch of 79 students were admitted for the academic year 2006/07 by the admission policy of University grants Commission. There is no any Faculty of this nature established in any other universities in Sri Lanka. Presently the University is operating with six Faculties namely Faculty of Arts and Culture (FAC), Faculty of Management and Commerce (FMC), Faculty of Applied Sciences (FAS), Faculty of Islamic Studies & Arabic Language (FIA), Faculty of Engineering (FE) and Faculty of Faculty of Technology (FT).