Background Traditional teaching methods such as lectures alone cannot meet educational needs in the medical sciences. It is necessary to supplement lectures with additional methods in order to prepare the students for problem solving in real situations. Objectives The present study aimed at employing the problem-based learning (PBL) method in the theoretical physiology of autonomic nervous system (ANS) course for medical students and comparing the results with the customary method of lectures. Methods In 2014, first-year medical students enrolled in the neurology curricular block at Tehran University of Medical Sciences were randomly assigned to two groups. One group participated in classes with lectures, while the other group was divided into subgroups of 10 for PBL sessions. In the first session of PBL, a scenario pertaining to ANS was presented, and then the students were asked to expand the scenario and discuss it using brainstorming method. The first session was held on introducing a reference for studying. In the second session, students in each group presented the results of their individual studies, and a representative from each group gave a report in line with the educational objectives of the class. Finally, a short-answer final test and survey were administered. Data were analyzed using independent samples t-test and Levene’s test. Results Based on results, mean scores of students in the PBL group (15.20 ± 3.31) were significantly higher than those of students in the lecture group (12.38 ± 4.49) (P < 0.001). Based on the survey, students preferred PBL to lectures. Conclusions PBL promotes motivation, self-confidence, and communication skills, all of which contribute to the better learning of the students who attended the theoretical physiology of ANS course.