BackgroundThe health system in South Sudan faces extreme domestic resource constraints, low capacity, and protracted humanitarian crises. Supportive supervision is believed to improve the quality of health care and service delivery by compensating for flaws in health workforce management. This study aimed to explore the current supervision practices in South Sudan and identify areas for quality improvement.MethodsThe study employed qualitative approaches to collect and analyse data from six purposefully selected counties. Data were collected from 194 participants using semi-structured interviews (43 health managers) and focus group discussions (151 health workers). Thematic content analysis was used to yield an in-depth understanding of the supervision practices in the health sector.ResultsThe study found that integrated supportive supervision and monitoring visits were the main approaches used for health services supervision in South Sudan. Supportive supervision focused more on health system administration and less on clinical matters. Although fragmented, supportive supervision was carried out quarterly, while monitoring visits were either conducted monthly or ad hoc. Prioritization for supportive supervision was mainly data driven. Paper-based checklists were the most commonly used supervision tools. Many supervisors had no formal training on supportive supervision and only learned on the job. The health workers received on-site verbal feedback and, most times, on-the-job training sessions through coaching and mentorship. Action plans developed during supervision were inadequately followed up due to insufficient funding. Insecurity, poor road networks, lack of competent health managers, poor coordination, and lack of adequate means of transport were some of the challenges experienced during supervision. The presumed outcomes of supportive supervision were improvements in human resource management, drug management, health data reporting, teamwork, and staff respect for one another.ConclusionSupportive supervision remains a daunting task in the South Sudan health sector due to a combination of external and health system factors. Our study findings suggest that strengthening the processes and providing inputs for supervision should be prioritized if quality improvement is to be attained. This necessitates stronger stewardship from the Ministry of Health, integration of different supervision practices, investment in the capacity of the health workforce, and health infrastructure development.