Severely malnourished patients can present with bilateral pitting oedema, which is a common sign of Kwashiorkor. However, bilateral pitting oedema can also be an expression of other pathologies. In Mali and DRC, the number of children presenting with bilateral pitting oedema at MSF (Médecins Sans Frontiers/Doctors Without Borders) hospitals are up to 30% (Mali) and 49% (DRC) higher than in other countries, however, the reasons underlying this trend are unknown. Through this qualitative study, we aimed to explore the perspectives and lived experiences of health professionals on the diagnosis and management of children with bilateral pitting oedema. Using a participatory approach, we conducted 21 in-depth interviews, and 2 focus groups with health professionals at MSF health facilities who had worked in the settings of Koutiala (Mali) and Rutshuru (DRC) for at least 6 months. The understanding of the bilateral pitting oedema phenomenon is complex. Health workers described clinical obstacles to reducing mortality, including: i) difficulties making the diagnosis due to a lack of specialized staff and insufficient resources, ii) challenges treating complications that may arise due to the complexity of the diseases associated with bilateral pitting oedema, and iii) lack of scientific evidence in the literature explaining the physiopathology of bilateral pitting oedema. Study participants shared several key recommendations for reducing mortality among children presenting with bilateral pitting oedema, including prevention of bilateral pitting oedema at the community level, standardization of the diagnostic process, strengthening of medical training, and better collaboration both within the medical teams and between teams and the children’s families.