Background Thus far, little work in bioethics has specifically focused on global health research priority-setting. Yet features of global health research priority-setting raise ethical considerations and concerns related to health justice. For example, such processes are often exclusively disease-driven, meaning they rely heavily on burden of disease considerations. They, therefore, tend to undervalue non-biomedical research topics, which have been identified as essential to helping reduce health disparities. In recognition of these ethical concerns and the limited scholarship and dialogue addressing them, we convened an international workshop in September 2015. The workshop aimed to initiate discussion on the appropriate relationship between global and national levels of health research priority-setting and to begin exploring what might be ethically required for priority-setting at each of those levels. Main text This paper comprises our reflections following the workshop. Its main objective is to launch a research agenda for the ethics of global health research priority-setting. We identify three domains of global health research priority-setting—scope, underlying values and substantive requirements, and procedural considerations. For each domain, specific research questions are highlighted and why they need to be explored is explained. Some preliminary thoughts and normative arguments as to how the research questions might be answered are also offered. For example, we provide initial ideas about the appropriate relationship between different priority-setting levels and what values and substantive considerations should guide or underpin global health research priority-setting as a matter of justice. Conclusion We anticipate that framing a new research agenda for the ethics of global health research priority-setting will spur ethicists, researchers, and policymakers to refocus their efforts on developing more rigorous and ethically sound approaches to priority-setting