Public Finance Management (PFM) practices influence the attainment of health system goals. PFM processes are implemented within the budget cycle which entails the formulation, execution, and monitoring of government budgets. Budget monitoring and accountability actors, structures, and processes are important in improving the efficiency of health systems. This study examined how the budget monitoring and accountability processes influence the efficiency of county health systems in KenyaWe conducted a qualitative case study of four counties in Kenya selected based on their relative technical efficiency. We collected data using in-depth interviews with health and finance stakeholders (n = 70), and document reviews. We analyzed data using a thematic approach, informed by our study conceptual framework. We found that weak budget monitoring and accountability mechanisms compromised county health system efficiency by a) weakening the effective implementation of the budget formulation and execution steps of the budget cycle, b) enabling the misappropriation of public resources, and c) limiting evidence-informed decision-making by weakening feedback that would be provided by effective monitoring and accountability. Devolution meant that accountability actors were closer to implementation actors which promoted timely problem solving and the relevance of solutions. Internal audit practices were supportive and provided useful feedback to health system managers that facilitated improvements in budget formulation and execution. The efficiency of county health systems can be improved by strengthening the budget monitoring and accountability processes. This can be achieved by increasing the population's budget literacy, supporting participatory budgeting, synchronizing performance and financial accountability, implementing the existent budget monitoring and accountability mechanisms, rewarding efficiency, and sanctioning inefficiency.