BACKGROUND: Funding for health research is intrinsically limited; therefore, priority-setting is necessary to optimise investments. Prioritisation is particularly important for epidemic and pandemic pathogens, as preparedness needs for hypothetical threats can be difficult to assess, and response during outbreaks requires accelerated decision-making. Exercises which prioritise epidemic and pandemic pathogens have been published; however, to our knowledge, there has been no systematic analysis of how, why and by whom these exercises are conducted. Guidelines and good practices for prioritisation exist, but whether these are followed for pathogen prioritisation and the consequences on the quality and impact of results has not yet been analysed. METHODS: We undertook a scoping review to investigate processes and methods of analysis reported across pathogen priority-setting exercises. We ran a grey literature search on Overton and Google to identify relevant resources published since 2018. The resources were screened by independent reviewers and extracted data were analysed using descriptive statistics and narrative synthesis. RESULTS: The identified pathogen prioritisation exercises varied in geographical scope and included exercises focusing on specific threats such as antimicrobial resistance, as well as all-hazard prioritisation activities. We identified differences in the types of participants involved and their roles in priority-setting processes. While a diversity of processes and methods of analysis exist, there were common practices and steps, notably identifying candidate priority pathogens and developing assessment criteria, and then scoring the former against the latter to reach a final priority list. There were commonalities in the criteria themes used to score pathogens, such as severity of disease, transmissibility, prevalence, impact and mitigation measures. Rabies and influenza A were the two most reported priority list pathogens. Our ability to synthesise a meaningful ordered priority list across publications was limited by discrepancies in taxonomy and scope. CONCLUSIONS: This study provides the first examination of priority setting exercises identifying high-consequence infectious pathogens. The review reveals important elements of commonality and variability between priority-setting exercises, highlighting areas for improvement to increase the comparability and quality of future efforts and their implementation.