BACKGROUND: After years of decline and disintegration, the Somalia Federal Government alongside international and domestic partners is beginning the process of rebuilding its national health system. In this study, we aim to shed light on the current approaches to health system strengthening, as viewed by stakeholders closely involved in its development. METHODS: Key informant interviews were undertaken with health and development professionals working within all three administrative regions of Somalia, as well as with Somali ministry of health officials, global health and policy specialists with interests in health system reconstruction in fragile states. A review of published and grey literature on Somalia, health systems, fragile and conflict-affected countries using PubMed and Reliefweb was also conducted. Technical documents designed for Somali health system building by external development partners were also reviewed. RESULTS: Key priorities identified by participants were, strengthening of local governance and management capacity, scaling-up efforts to structure a robust health financing mechanism, engagement with the burgeoning and dynamic private sector, as well as investing in the appropriate human resources for health. CONCLUSIONS: The study found that there was widespread agreement among participants that health system strengthening through a coordinated system would improve long-term capacity in Somalia's health sector. Future research should focus on the evaluation of the modalities by which health system strengthening interventions are implemented, on neglected topics such as mental health within the Somali health system, as well as on population-level barriers to accessing health systems.