Background: All countries face challenging decisions about healthcare coverage. The scare resources of low income countries prevent improvements in equitable access and quality. Malawi, one of the poorest countries in the world, has committed to achieving Universal Health Coverage (UHC) by 2030. The health sector is highly dependent on donor contributions, but recent poor governance of government-funded healthcare saw donors withdraw funding, limiting services and resources. The 2017 updated National Health Plan II and accompanying Health Strategic Plan II identify the importance of improved governance and strategies to achieve it, including greater harmonisation with health stakeholders. This study explores health sector stakeholders’ perceptions of challenges to improving governance in the national health system. Methods: A qualitative study design was used. Interviews were conducted with 22 representatives of the major international and faith-based non-government organisations, civil society organisations, local government and government-funded organisations, and governance bodies operating in Malawi. Open questions were asked about experiences and perceptions of the functioning of the health system and healthcare decision-making. The transcripts and field notes were analysed using inductive content analysis.Results: Stakeholders view governance challenges as a barrier to achieving a more effective and equitable health system. Three types of challenges were identified: accountability (enforceability; answerability; stakeholder-led initiatives); health resource management (healthcare financing; drug supply); influence in decision-making (unequal power; stakeholder engagement).Conclusions: Health sector stakeholders see a range of serious challenges to improving governance in the national health system in Malawi which will impact on the government’s goal of achieving UHC by 2030. These can be categorised as political, structural, and financial challenges. Stakeholders identify the need for improved oversight, implementation, service delivery and social accountability of government-funded service providers to communities. Eighteen months after the introduction of the NHP II and HSSP II, they see little evidence of improved governance and have little or no confidence in the government’s ability to deliver UHC in the timeframe set out by the Sustainable Development Goals (SDGs). The difficulties stakeholders perceive in relation to building equitable and effective health governance in Malawi have relevance for other resource-limited countries which have also committed to the goal of UHC.