As global trade of live animals expands, there is increasing need to assess the risks of invasive organisms, including pathogens, that can accompany these translocations. The movement and release of live baitfish by recreational anglers has been identified as a particularly high-risk pathway for the spread of aquatic diseases in the United States. To provide risk-based decision support for preventing and managing disease invasions from baitfish release, we developed a hazard identification and ranking tool to identify the pathogens that pose the highest risk to wild fish via this pathway. We created a screening protocol and semi-quantitative stochastic risk ranking framework, combining published data with expert elicitation (n = 25) and applied the framework to identify high-priority pathogens for the bait supply in Minnesota, USA. Normalized scores were developed for seven risk criteria (likelihood of transfer, prevalence in bait supply, likelihood of colonization, current distribution, economic impact if established, ecological impact if established and host species) to characterize a pathogen’s ability to persist in the bait supply and cause impacts to wild fish species of concern. The generalist macroparasite Schizocotyle acheilognathi was identified as presenting highest overall threat, followed by the microsporidian Ovipleistophora ovariae, and viral haemorrhagic septicaemia virus. Our findings provide risk-based decision support for managers charged with maintaining both the recreational fishing industry and sustainable, healthy natural resources. Particularly, the identification of several high-risk but currently unregulated pathogens suggests that focusing risk management on pathogens of concern in all potential host species could reduce disease introduction risk. The ranking process, implemented here for a single state case study, provides a conceptual framework for integrating expert opinion and sparse available data that could be scaled up and applied across jurisdictions to inform risk-based management of the live baitfish pathway.