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Interest in climate engineering research has grown rapidly owing to the slow progress of international climate negotiations. As some scientists are proposing to expand research and conduct field tests, there is an emerging debate about whether and how it should proceed. It is widely accepted both by the supporters and critics that public engagement from the early stage of research is necessary. Nonetheless, most, if not all, of existing research projects of climate engineering were designed predominantly by experts. To produce socially relevant knowledge, and hence, pursue transdisciplinary research that integrates interdisciplinary research and public engagement, it is desirable for scientists to decide together with the public on what kind of research should be done. In this paper, we both as Japanese scientists and stakeholders collaboratively identify 40 socially relevant research questions on climate engineering with a particular emphasis on stratospheric aerosol injection, using a method designed to encourage science–policy collaboration. While we acknowledge some methodological problems and the difficulty in obtaining active participation from stakeholders, the list of identified questions covers broad interdisciplinary perspectives and diverse interests, and may provide an important foundation for future transdisciplinary research on climate engineering. Given the dynamic nature of climate change and policy responses, research agendas should be periodically and iteratively reviewed and updated through transdisciplinary processes.