The Siddha system of medicine is the most ancient medical systems in India and has a long history of traditional practice in South India and Sri Lanka. The Siddha medical system plays a prominent role in the traditional healthcare system in the Northern and Eastern parts of Sri Lanka. Nowadays, the world has turned its attention towards traditional medical systems. The Siddha medical system is deeply rooted in the Eastern province and has been a long-felt need for the people residing in the Eastern part of Sri Lanka. This need arises from the fact that the father of Siddha medicine, Saint Ahathiyar, set his foot and established an Ahathiyar sthapanam (Ancient University for 64 Tamil arts including Siddha medicine) in Kanguveli, Muthur, which is evidenced by Thirukarasaipuranam.

This vibrant energy led the late Ms. K. Thangeswary, an honourable ex-member of the Parliament, to advocate for the establishment of the Faculty of Siddha Medicine at Eastern University. This advocacy was initiated through a request letter from the Eastern Province Siddha Medical Physicians Association in 2004.

Afterward, the Council of Eastern University discussed and handed over this subject to Trincomalee Campus to establish this faculty at the Trincomalee Campus. At this juncture, Dr. N. Varnakulendran, a Consultant Physician at Kappalthurai Ayurveda Hospital, served as an Academic Consultant to develop the proposal and curriculum for setting up the Siddha faculty. Subsequently, the proposal was approved at the 175th Council of Eastern University, marking a new step in 2015 towards establishing the Faculty of Siddha Medicine at Trincomalee Campus.

After several lengthy discussions in the Standing Committee of Indigenous Medicine since 2007, the University Grants Commission offered the Bachelor of Siddha Medicine and Surgery (BSMS) degree to commence the program under the existing faculty from the Academic year 2007/2008, initially enrolling 20 students. In this circumstance, since the Siddha system is a distinct medical field, the existing faculties at Trincomalee Campus were not able to accommodate it within their faculty. Later, the Standing Committee of Indigenous Medicine decided to function as a unit under the purview of the Rector, similar to the setup of the University of Jaffna. The later, during the 247th Council held in 2017, a decision was made to attach the Unit of Siddha Medicine with the Faculty of Applied Science to address the issue of degree awarding.

The Siddha Medicine course comprises 5 years of coursework, laboratory work, research, and clinical training. The initial intake was twenty (20) students in the academic year 2007/2008, and now it has increased to 75 students starting from the academic year 2015/2016. Among the 10 academic staff members, six hold the position of Senior Lecturer 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 the year 2008. Following several steps of the official procedure, the project was approved by the Government of India, which generously 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, including Anatomy, Physiology, Biochemistry, Gunapadam, Medicinal Botany, Pharmacy, and the Analytical Research Laboratory with sophisticated instruments. The next milestone was the acquisition of a 7-acre government land to establish a Teaching Hospital for the teaching of Siddha Medicine at Konesapuri, nearest to the campus where a small hospital is functioning with OPD facilities.

The BSMS program at the Unit of Siddha Medicine starts with a semester-based curriculum. The aim is to enhance graduates to become efficient and effective Siddha medical professionals who can serve the community. Therefore, the BSMS program integrates both teacher-centered approaches (classroom lectures) and student-centered learning methods, such as self-directed learning (SDL), group works, presentations, clinical training, practical, field-based projects, and research projects. After graduation, students are required to undergo a one-year internship at a government Indigenous medical hospital. Upon successful completion of the internship, they need to register with the Ayurveda Medical Council to obtain a registration number, allowing them to provide medical care to patients.

According to the Gazette of the Democratic Socialist Republic of Sri Lanka notification on 14th July 2023, the Unit of Siddha Medicine was upgraded to the Faculty of Siddha Medicine with three departments; the Department of Moolathaththuvam (Basic Philosophy), the Department of Gunapadam (Siddha Pharmacology) and the Department of Noinaadal Chikitsai (Pathology and Clinical Sciences).