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Background Bullying of medical students by clinicians is a common problem in medical education that has adverse effects on student psychological well-being, educational experiences and professional development. The hierarchical structure, power imbalances and historical teaching practices present in South African medical schools may contribute to an environment where that mistreatment occurs, but limited synthesis of the evidence exists in relation to South Africa.Aim The aim of this scoping review is to review and map existing literature related to the bullying of medical students by clinicians in South African medical training contexts, including the forms, prevalence, contributing factors, consequences and how institutions respond.Methods and analysis The authors will execute this scoping review in conformity with the Joanna Briggs Institute manual for evidence synthesis and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Review (PRISMA-ScR) guidelines. This will be a mixed-method scoping review that incorporates both qualitative and quantitative studies. The review process and procedures will include a search in databases such as PubMed, Cumulative Index to Nursing & Allied Health Literature, Scopus, Web of Science, Psych-Info and African Journals Online (AJOL). Socioecological model is a model that incorporates multiple behaviour change across five domains. The review is expected to take 10 months to complete, commencing on 10 November 2025 and concluding on 10 September 2026. Thematic analysis will be conducted with NVivo data management software.PROSPERO registration number CRD420251179182.