Background: The ever-increasing development of information and communication technologies has created new opportunities in the domains of curriculum planning and teaching. In this study, an exercise therapy course was held using both lecture-based and virtual teaching methods. Then, the students’ opinions were investigated and their overall levels of satisfaction were measured. Methods: This cross-sectional study was conducted among all physiotherapy students who had enrolled in the fourth semester of 2014 academic year and had selected the course of principles of exercise therapy. This study was conducted during one semester. We evaluated the effect of lecture-based and virtual (multimedia-based) methods of education according to the learning management system (LMS) among 20 students. A researcher-made questionnaire was designed regarding satisfaction with virtual versus lecture-based teaching methods; the questionnaire was scored based on a five-point Likert-type scale. Results: Of 20 students, one individual was single and 19 were married. Moreover, the mean test score was 12.38 ± 3.23 for the virtual teaching method, while it was 14.21 ± 1.88 for the lecture-based one, showing a significant difference (P = 0.03). Generally, 50% of the students preferred the virtual teaching method over the lecture-based one. In total, 75% of the students were satisfied or totally satisfied with the virtual teaching method for the exercise therapy course. Conclusions: In terms of scores, the lecture-based method was better than the virtual one. However, the level of student’s satisfaction in the virtual method was higher than the lecture-based one.