Background Effective Public Financial Management (PFM) approaches are imperative in the quest for efficiency in health service delivery. Reviews conducted in this area have assessed the impact of PFM approaches on health system efficiency but have left out the mechanisms through which PFM influences efficiency. This scoping review aims to synthesize evidence on the mechanisms by which PFM influences health system efficiency. Methods We searched databases of PubMed and Google Scholar and websites of the World Health Organization (WHO), World Bank and Overseas Development Institute (ODI) for peer-reviewed and grey literature articles that provided data on the relationship between PFM and health system efficiency. Three reviewers screened the articles for eligibility with the inclusion criteria. Data on PFM and health system efficiency was charted and summarized. We then reported the mechanisms by which PFM influence efficiency. Results PFM processes and structures influence health system efficiency by influencing; the alignment of resources to health system needs, the cost of inputs, the motivation of health workers, and the input mix. Conclusion The entire budget process influences health system efficiency. However, most of the findings are drawn from studies that focused on aspects of the budget process. Studies that look at PFM in totality will help explore other cross-cutting issues within sections of the budget cycle; they will also bring out the relationship between the different phases of the budget cycle.