The Faculty of Medicine, University of Jaffna was established in October 1978 at the buildings obtained from the Ayurveda Hospital at Kaithady, about 10 kilometers from Jaffna town on the A9 road.  The Department of Physiology also was established at the same time along with other Departments with a small laboratory and four rooms for the staff.  The ground floor of the faculty building complex at Thirunelvely, about one kilometre from the main university, was taken over in 1982 and the Department shared the space with Department of Biochemistry until the dedicated space for physiology in the first floor was handed over in 1987.  Dr.  S. V. Parameswaran [later promoted as Professor] who came from the Department of Physiology at the Faculty of Medicine, Peradeniya was appointed as the first Head of the Department and he developed the department and its curriculum under the guidance of Professor V. Basanayake of Peradeniya. Unfortunately, the Department experienced loss of all its equipment twice, once in 1987 and again in 1996 due to the displacements as a result of the war situation prevailed.

Many staff members were recruited into the department but most of them left because of the difficulties related to the war situation prevailed.  Prof. S. V. Parameswaran continued to serve in the Department until he retired in 2007.  He served as the Dean of the Faculty for 3 years from 1994.

Dr. K. Sivapalan who joined the department in 1981 worked for his PhD in the University of Leeds, UK from 1984 to 1987, promoted to Senior Lecturer and again left due to displacement in 1997, reinstated in 2002 and promoted as Associate Professor.  He served for the faculty for 10 years as Clinical Coordinator from 2012 and Dean of the Faculty for 9 years from 2013 in addition to teaching Physiology for medical and AHS students.  He continues to teach on assignment basis after his retirement in 2017.

Dr.D.Gunarajasingam, a Veterinary graduate, joined the Department of Physiology in 1985 with M.Phill degree as a Probationary Lecturer. In 1997 he completed the Ph.D. program as a full-time student and promoted to senior lecturer. He involved in teaching MBBS and Allied Health Science students and Public Health Inspectors.  He retired in 2017 and continues to teach under assignment appointment.

Dr. (Mrs) M. Sooriyakanthan served the department from July 2010 as a temporary lecturer and then recruited as probationary lecturer in September 2012. She has completed Post Graduate Diploma in Medical Physiology at PGIM, Colombo in 2016. She obtained her PhD from University of Sri Jayewardenepura in 2020 and promoted to Senior Lecturer from July 2020 and appointed as the Head of the Department.

Dr. Kausala Sithamparapillai joined the department in 2021. She has completed MD in Clinical Nutrition at the Post Graduate Institute of Medicine, Colombo. She is a Consultant Nutrition Physician & Lecturer in Physiology.

In 2024, three probationary lecturers; Dr. Sunthareswaran Vithyasahar, Dr. Shythaky Jeyarajah, Dr. Deneshan Peranantharajah were recruited as probationary lecturers in Physiology.

In addition to teaching medical students, the department was involved in teaching physiology for AMP students during the years 1979 to 1987 when the Ministry of Health requested the faculty to undertake the AMP training course.  When the Siddha section of Indigenous Medicine was displaced from Colombo in 1984 and became a part of the University of Jaffna, Siddha students were taught physiology by the staff of the Department of Physiology until they developed their own staff and laboratories.  Since the commencement of Allied Health Sciences in 2006, the Department is engaged in teaching basic physiology to the AHS students.

The heavy undergraduate teaching load, war situation and displacements with loss of equipment and lack of staff made the department to limit its work towards undergraduate teaching but the staff members were involved in limited research activities.  After the winning the QEF grant from the World Bank in 2006, the teaching and research activities are improved.

The department has been providing service function tests in carrying out Lung function test, nerve conduction studies and in perimetry tests.

At present it is planning to assist in conducting Lung function tests to Chest Clinic at Teaching Hospital Jaffna and to provide pulmonary rehabilitation for patients with respiratory disease.