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Purpose To estimate the incidence of shoulder disorders in a cohort of Health Care Workers (HCWs). Methods 4406 workers employed from 2009 to 2020, were included in the study. Occupational risk factors and jobs were assessed according to working history. Incident cases were defined in case of shoulder pain associated with functional limitations during the medical examination. The Cox regression model was used to calculate the Hazard Ratio (HR) for different work activities, adjusted for age, sex, body mass index, and previous musculoskeletal injuries, using clerks as the reference category. Results The incidence rates of shoulder musculoskeletal disorder for men and women were 13.1 for 1000 person-years (CI 95% 10.6–16.3) and 20.1 for 1000 person-years (CI 95% 17.8–22.6) respectively. The adjusted HR was significantly increased with age (1.06, CI 95% 1.05–1.07), outpatient health activities (2.82, CI 95% 1.89–4.219), and wards health activity (2.37, CI 95% 1.68–3.33). Conclusion HCWs with high biomechanical risk such as nurses and healthcare assistants had a higher incidence of shoulder disorders. Actions are needed for better prevention in health care assistance.