Siddha system Medicine is the most ancient medical systems of India and has a long history which had been practiced traditionally in south India and Srilanka. The Siddha Medical system plays a prominent role in traditional health care system in the Northern and Eastern parts of Sri Lanka. Now a days globe has turn its eyes towards the traditional medical system. The siddha medical system very deep rooted system in Eastern province and long felt need of the people who dwell in Eastern part of Srilanka because the father of Siddhamedicine Saint Ahathiyar set his foot  and established a Ahathiyar sthapanam(Ancient university for 64 tamil arts including siddha medicine) at Kanguveli Muthur which is evidenced by Thirukarasaipuranam This vibrant energy brought Honorable ex.Member of the Parliament Late Ms. K. Thangeswary in to this scene and she put a claim on Eastern University to establish the Faculty of Siddha Medicine at Eastern University with the request letter of Eastern Province Siddha Medical Physicians Association in 2004. Thereafter the Council of Eastern University discussed and handed over this subject to Trincomalee Campus to establish this faculty at Trincomalee Campus. In this juncture, Dr. N. Varnakulendran, Consultant physician, Kappalthurai, Ayurveda Hospital served as an Academic consultant to develop the proposal and curriculum to set up siddha faculty. Then the proposal has been approved at 175^thCouncil of Eastern University embodied a new step in 2015 towards building up the Faculty of Siddha Medicine in Trincomalee Campus. The several lengthy discussion in standing committee of Indigenous medicine since 2007,the university grant commission offered Bachelor of Siddha Medicine and Surgery (BSMS) degree to commence the program under existing faculty from the Academic year 2007 / 2008 with the student number 20  initially. In this circumstance, since the siddha system is a medical field the existing faculties at Trincomaleecampus were not in a position to accommodate into their faculty. Later the standing committee of Indigenous medicine decided to function as unit under purview of Rector in par with university of Jaffna set up. The later on the 247^th Council held on 2017 decided to attach the Unit of Siddha Medicine with the Faculty of Applied Science to solve the degree awarding issue. Siddha Medicine course comprises 5 years of course work, Laboratory work, research work and clinical training. The initial intake was twenty (20) students in the academic year 2007/2008 and now it has now increased up to 75 from the academic year 2015/ 2016. Among 10 academic staff members six are in Senior Lecturer grade in Siddha Medicine.

A project for setting up a Faculty of Siddha medicine was submitted to the High Commission of India through the proper channels in year 2008. Followed by several steps of official procedure the project was approved by Govt. of India and thus donated office equipment, laboratory equipment, teaching aid equipment, furniture, books and two vehicles in November 2010. Based on this Indian project the main six laboratories were established such as Anatomy, Physiology, Biochemistry, Gunapadam, Medicinal botany, Pharmacy and Analytical research laboratory with sophisticated instruments. The next mile stone was obtained 7 acre government land to establish the Teaching Hospital teaching of Siddha Medcine at Konesapuri nearest to campus where small hospital is functioning with OPD facility.

BSMS programme at Unit of Siddha Medicine starts with semester based curriculum. The aim is to enhance the graduates to be efficient and effective Siddha medical graduates to provide the service to the community. Therefore, the BSMS program integrates teacher centered (class room lecturers) and student-centered learning as SDL, group works, presentation, clinical training, practical, field-based projects and with research project. Subsequent to graduation they have to undergo one year internship in government Indigenous medical hospital. After successful completion of internship they have to register at Ayurvedic medical council to obtain register number to treat the patients.