Background: While leading AIDS organizations expect faith and health collaborations to play a crucial role in organizing and scaling up community-based HIV services, it is unclear how this can be realized. Little primary research has been conducted into which strategies for collaboration and service provision are most effective, efficient, scalable and sustainable. Seeking to align research with urgent needs, enhance coordination and increase the likelihood that results are used, this study aimed to set an inclusive global research agenda that reflects priority research questions from key stakeholders at the intersection of HIV healthcare and faith. Methods: In order to develop this global research agenda, we drew from document analyses, focus group discussions, interviews with purposively selected key informants from all continents (policy-makers, healthcare providers, faith leaders, academics and HIV activists), an online questionnaire, and expert meetings at several global conferences. We carried out focus group discussions and interviews with faith leaders in South Africa. Other stakeholder focus groups and interviews were carried out online or in person in France, Switzerland, the Netherlands and South Africa, and virtual questionnaires were distributed to stakeholders worldwide. Respondents were purposively sampled. Results: We interviewed 53 participants, and 110 stakeholders responded to the online questionnaire. The participants worked in 54 countries, with the majority having research experience (84%), experience with policy processes (73%) and/or experience as a healthcare provider (60%) and identifying as religious (79%). From interviews (N = 53) and questionnaires (N = 110), we identified 10 research themes: addressing sexuality, stigma, supporting specific populations, counselling and disclosure, agenda-setting, mobilizing and organizing funding, evaluating faith-health collaborations, advantage of faith initiatives, gender roles, and education. Respondents emphasized the need for more primary research and prioritized two themes: improving the engagement of faith communities in addressing sexuality and tackling stigma. Conclusions: A wide range of respondents participated in developing the research agenda. To align research to the prioritized themes and ensure that results are used, it is essential to further engage key users, funders, researchers and other stakeholders, strengthen the capacity for locally embedded research and research uptake and contextualize priorities to diverse religious traditions, key populations and local circumstances.