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The University of Jaffna was first established in 1974, as the Jaffna Campus of the University of Sri Lanka, offering courses in science and humanities. First batch of 104 students were admitted in October 1974. In 1978,with the implementation of the universities Act no. 16 of 1978, it became an independent and autonomous university as the University of Jaffna. Faculty of Medicine was established at Kaithady in October of 1978, and 70 students were admitted to it. The Medical faculty was subsequently moved to join the other faculties on the Thirunelvely site. The Agriculture faculty was established in Kilinochchi in 1990 and foundation for Engineering faculty was laid in 1995. The main campus of the University is located in Thirunelvely in Jaffna (pop. ~110 000) in a 43 acre campus.

Jaffna University has six faculties (Faculties of Agriculture, Arts, Graduate Studies, Management Studies and Commerce, Medicine, and Science), the Vavuniya Campus of the University of Jaffna and its two faculties
(Faculties of Applied Science and Business Studies), the Library, the Ramanathan Academy of Fine Arts, Department of Siddha Medicine, the Sports Science Unit, the Health Studies Unit, the Physical Education Unit, the External Examinations Unit, the Workers Education Unit, the Extra Mural Studies Unit, the Computer Unit and the Centre for Development of Fisheries.