Health policy and systems research (HPSR) is vital to guiding global institutions, funders, policymakers, activists and implementers in developing and enacting strategies to achieve the Sustainable Development Goals. We undertook a multi-stage participatory process to identify priority research questions relevant to improving accountability within health systems. We conducted interviews (n = 54) and focus group discussions (n = 2) with policymakers from international and national bodies (ministries of health, other government agencies and technical support institutions) across the WHO regions. Respondents were asked to reflect on challenges and current policy discussions related to health systems accountability, and to identify their pressing research needs. We also conducted an overview of reviews (n = 34) to determine the current status of knowledge on health systems accountability and to identify any gaps. We extracted research questions from the policymaker interviews and focus groups (70 questions) and from the overview of reviews (112 questions), and synthesized these into 36 overarching questions. Using the online platform Co-Digital, we invited researchers from around the world to refine and then rank the questions according to research importance. The questions that emerged amongst the top priorities focused on political factors that mediate the adoption or effectiveness of accountability initiatives, processes and incentives that facilitate the acceptability of accountability mechanisms among frontline healthcare providers, and the national governance reforms and contexts that enhance provider accountability. The process revealed different underlying conceptions of social accountability and how best to promote it, with some researchers and policymakers focusing on specific interventions and others embracing a more systems-oriented approach to understanding accountability, the multiple forms that it can take, how these interact with each other and the importance of power and underlying social relations. The findings from this exercise identify HPSR funding priorities and future areas for evidence production and policy engagement.