Abstract Aims/hypothesis Research agendas are typically set by researchers and funders, meaning that priorities of end users, such as patients and healthcare professionals (HCPs), could be missed or overlooked in research. To ensure future research in prediabetes is of relevance and benefit to people with prediabetes and HCPs, it is important to involve these stakeholders in setting the research agenda. The aim of this study was to establish a top-10 list of the most important research questions in prediabetes (HbA1c 42–47 mmol/mol [6.0–6.4%]) by involving and collaborating with patients, relatives, patient organisations, HCPs and researchers. Methods We used a modified James Lind Alliance Priority Setting Partnership methodology, following the four-step process including: (1) Gathering uncertainties; (2) Organising uncertainties; (3) Interim priority setting; and (4) Final priority setting in a workshop. Further, the international relevance of the final top-10 list was assessed. Results A total of 1142 responses were submitted by 405 people to: ‘What questions about prediabetes would you like to see answered by research?’. The collected uncertainties were categorised and condensed into 35 indicative questions. Through prioritisation, patients and relatives had different preferences from researchers and HCPs. The jointly agreed top-10 list included questions on prevention strategies, risk factors, diet advice, screening and personalised treatment. Highest prioritisation was given to: ‘What is the best prevention of diabetes and will early prevention strategies reduce the number of people with type 2 diabetes?’. Conclusions/interpretation An iterative and collaborative process identified shared priorities between patients, HCPs and relevant stakeholders in prediabetes. Findings should support academia, funders and the healthcare industry to target research within prediabetes specifically to the needs of patients and HCPs. Graphical Abstract