Background: Musculoskeletal disorders is defined as a musculoskeletal strain reported by an individual. Physical activity prevents many disabling diseases and musculoskeletal disorders. Low level of physical activity is associated with a higher prevalence of musculoskeletal disorders. In Saudi Arabia and among medical students, lowest rates of physical activity were found. Our aim is to assess the prevalence of musculoskeletal disorders and its correlation to physical activity. Methods: A cross-sectional study of 392 health specialty students in Taif University was carried out from January 1 to March 1, 2018, using a predesigned questionnaire, including demographic characteristics, an International Physical Activity Questionnaires–short form to assess the level of physical activity, and Standardized Nordic Questionnaires for the analysis of musculoskeletal symptoms. Results: Our study found that 64.8% of the students had musculoskeletal disorders. The highest prevalence was among medical students; 48.4% of them were having musculoskeletal disorders ( P < 0.05). The most frequent region was the lower back (33.4%). There is a significant association between the musculoskeletal disorders and the level of physical activity, with 42.9% of the students with a moderate level of physical activity having musculoskeletal disorders ( P < 0.05). Conclusions: The prevalence of musculoskeletal disorders is higher among medical than pharmacy and health science students. Most of the affected students were having a moderate level of physical activity. Psychosocial stress seems to be a major contributor to musculoskeletal disorders, rather than physical activity level.