Introduction Video-based learning has gained prominence in medical education and, more recently, in musculoskeletal teaching. This study investigated medical students’ perceptions of the effectiveness of online video-based learning for musculoskeletal physical examination skills. Methods For one academic year, undergraduate medical students were instructed online through video-based learning before bedside teaching about the physical examination of knee and shoulder joints. At the end of the course, the students participated in a survey to assess their perceptions of the online video-based learning module using a pre-validated questionnaire. The questionnaire consisted of closed-ended and open-ended questions. The closed-ended question responses were assessed using a Likert scale; the open-ended responses were analyzed qualitatively. Results In total, 242 out of 310 students who participated in the online video-based learning responded to the survey. Most students found the teaching approach to be satisfactory and preferable to traditional teaching methods. However, they also felt that these modules could not replace hands-on practice. The most helpful aspects of the training modules were a better understanding of the specific tests, technique, and sequence of administering the physical examination. Perceived limitations included the inadequately addressed theoretical basis of the physical examination and the special tests, the need for more time to explain clinical anatomy, and the practical implications of the positive special tests. Conclusion Undergraduate medical students perceive VBL as helpful for MPES learning. The positive aspects of the VBL approach in teaching MPES are that it is comprehensive, easily accessible, offers standardized teaching, save times, and it includes demonstrations of special tests, examination techniques, and the sequence and organization of the clinical examination. The main perceived limitations were lack of content regarding clinical reasoning and the anatomical basis of the clinical tests.