Background: Recently graduated South African medical practitioners (interns) are expected to be efficient and resilient in limited resource contexts that face multiple disease burdens. Work-based assessment in SA internship focuses on clinical skills and neglects the evaluation of non-clinical skills. This sub-optimal assessment process creates a daunting task for clinician supervisors who are expected to certify these interns for independent practice. Methods: Using a mixed methodological approach, the study sampled a cross section of 411 interns in seven hospitals in KwaZulu-Natal and their intern supervisors . Data collection methods included focus groups discussions and surveys. A 4-round modified Delphi-process was followed to reach consensus on the set of core competencies required. The assessment tool that resulted in the process included a variety of competencies and the tool was validated through factor analysis and internal consistency was measured with Cronbach’s alpha. Results : A competency-based assessment tool was developed that allows for the assessment of both clinical and non-clinical skills. This tool was found to be very reliable, with an overall Cronbach alpha of 0.927. Factor analysis for the instrument revealed 61 observable clinical activities aggregated into entrustable professional activities and these measured four major factors. The factors correspond with procedural clinical skills; holistic-care skills; and emotional skills related to social competence and self-management. Conclusion: A locally relevant competency-based assessment tool was developed in SA to assess local paediatric interns. The validated tool’s function as a multidimensional instrument to assess both clinical and non-clinical skills included the assessment of emotional skills which are largely neglected. Validated work-based assessment instruments can be developed that are responsive to local needs and support the development of holistic clinicians in high disease-burdened contexts.