Given the focus on health systems in the post-millennium development goal era and moving towards the sustainable development goals, there is a compelling need for a common framework for health policy and systems research ethics to guide researchers and facilitate review by research ethics committees. A consultation of global health policy and systems research and ethics experts was convened to identify ethical considerations relevant to health policy and systems research based on existing knowledge and to identify knowledge gaps through a scoping review and further expert deliberation. Health policy and systems research is highly complex and, in the absence of guidance documents, there is significant variability in ethics review. Although fundamental ethical principles pertain to both traditional clinical research and health policy and systems research, the application of these principles requires a comprehensive understanding of the nature of health policy and systems research with its distinct challenges. Such awareness must be raised among researchers and research ethics committees. Current research ethics committees lack familiarity with health policy and systems research and because health policy and systems research is conducted in real-world contexts, committees often have difficulties in determining whether a project is indeed research and/or requires ethical review. Given the strong current focus on health policy and systems research to rapidly improve health and health systems functioning globally, greater engagement and dialogue around the ethical concerns is required to optimise research review and research conduct in this rapidly evolving field.