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The Eastern University, Sri Lanka, was established on the 1st of October 1986 by a University Order dated 26th September 1986 issued under section 2 of the Universities Act No.16 of 1978. The University was preceded by the Batticaloa University College established on 1st August 1981.

The Batticaloa University College itself was established to fill a long felt need for the development of a Higher Education Institution in the Eastern Province. Its establishment was recommended by a Committee appointed by the University Grants Commission headed by Professor V.Appapillai, retired Professor of Physics and Dean of Science, University of Peradeniya and included Professor R.S.Ramakrishna, Professor Y.D.A.Senanayake, Professor S.T.Fernando, Mr.S.H.M.Jameel and Mr.Dixon Nilaweera.

Mr.K.W.Devanayagam, who at the time was Member of Parliament for Kalkudah electorate and Minister of Justice, took a personal interest in the establishment of the Batticaloa University College. The University College was established in the premises of the Vantharumoolai Madhya Vidyalayam, a school built by the late Mr.V.Nalliah, Minister for Posts and Telecommunication, Member of Parliament for Kalkudah electorate and Member of the Senate Council for Batticaloa North. The buildings had been badly damaged by cyclone of 1978 and were repaired and progressively restructured to suit the purposes of a new University College. In addition, over 100 acres of land have been added to the original campus. Student hostels and staff quarters have been constructed on this land and many new buildings are planned.
The Batticaloa University College began with two Faculties, namely the Faculty of Science and the Faculty of agriculture. Both these faculties were affiliated to the University of Peradeniya. Professor S.Rajaratnam was appointed as the Director of the College and he functioned in this capacity until February 1985. Mr.K.Rajendra functioned as the first Secretary of the College. He was succeeded by Mr.P.Sangaravel in June 1983.

Professor K.D. Arulpragasam appointed as Professor S.Rajaratnam as Director of the College in April 1985. He successfully negotiated upgrading of the University College to an independent University and was appointed the first Vice-Chancellor, when the University came into being in October 1986. Mr.S.H.M.Jameel was appointed as the first Registrar of the University.

Two new Faculties viz, the Faculty of Commerce & Management with the Department of Economics, Commerce & Management, and the Faculty of Cultural Studies with the Departments of Arabic, Islamic studies and Fine Arts were established in 1988. The Faculty of Cultural Studies was then expanded to include the Department of Languages, the Department of social Sciences and the Department of Geography and renamed the Faculty of Arts and Culture in 1991.
The Eastern University has recently obtained the approval to establish the Faculty of Health-Care Sciences and the students are admitted to this faculty from 2006 onwards. A Campus of the Eastern University functions at Trincomalee with the Faculties of Applied Sciences and Communication and Business Studies. Swami Vipulananda College of Music and Dance at Kallady, Batticaloa is attached to the Eastern University and renamed as Swami Vipulananda Institute of Aesthetic Studies where Degree Programmes in Music and Dance are conducted.

The Eastern University of Sri Lanka (EUSL), located in Chenkalady 12 km north of Batticaloa, was founded in 1980. Its development has been interrupted by the civil war. It is the cultural and economic focal point of the district of Batticaloa and extends its influence towards Trincomalee as well.