The physician assignment and course timetabling problem at medical universities is a generalized version of the academic timetabling problem. This problem entails assigning courses, educational and clinical tasks to physician faculty members over a semester or academic year. The problem of timetabling academic courses and scheduling physicians in a hospital has been investigated independently in previous studies in this field. These two fields of research are brought together in this article through the presentation of a multi-objective Mixed-Integer Linear Programming (MILP) model. The proposed model is based on two optimization criteria: minimizing workload imbalance and maximizing physician preferences. The model is applied to a case study involving the assignment of physicians to courses, educational and clinical tasks at Kurdistan University of Medical Sciences' Department of Infectious Diseases. Pareto solutions are obtained using an enhanced version of the augmented epsilon constraint implemented in the General Algebraic Modeling System (GAMS) optimization software; one is selected as the most desirable solution using the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) method. The proposed model is generic and could be adapted for use in other departments or medical schools.