Basic medical sciences course is one of the important courses in medical education that motivating and improving the educational process can be effective in promoting students' education. The aim of the present study was to evaluate and compare face-to-face education with e-learning on the score average of different lessens of medical students of Qom University of Medical Sciences and their level of satisfaction. In this study, 360 medical students participated which 180 students received face-to-face training and 180 students underwent virtual or e-learning. Then, the average final scores in 17 basic science lessons of students were compared in face-to-face and virtual groups. Also, a questionnaire was prepared whose validity was obtained by teachers and its reliability was obtained using Cronbach's alpha coefficient of 0.92. In the questionnaire, questions about students' learning and satisfaction were asked. Data analysis was performed using SPSS software and independent t-test. The mean score of the final exam in some lessons in the group undergoing virtual education was significantly higher than the average of the control group (P ≤ 0.05). In the questionnaire review, most of the students were satisfied with the volume of presented lessons and holding virtual exams but 78% of students were opposed to the full replacement of virtual education with face-to-face education. In general, virtual education cannot be a complete alternative to face-to-face education, but with the provision of a suitable platform, virtual education is offered as a complement to face-to-face education.