Emerging and re-emerging zoonotic diseases pose a significant threat to global health and economic security. This threat is further aggravated by amplifying drivers of change, including climate hazards and landscape alterations induced by climate change. Given the complex relationships between climate change and zoonotic disease health outcomes, a structured decision-making process is required to effectively identify pathogens of greatest concern to prioritize prevention and surveillance efforts. Here, we describe a workshop-based expert elicitation process in six steps to prioritize climate-sensitive zoonoses based on a structured approach to defining criteria for climate sensitivity. Fuzzy analytical hierarchy process methodology is used to analyze data provided by experts across human, animal, and environmental health sectors accounting for uncertainties at different stages of the prioritization process. We also present a new interactive expert elicitation interface that facilitates data collection and real-time visualization of prioritization results. The novel approach presented in this paper offers a generalized platform for prioritizing climate-sensitive zoonoses at a national or regional level. This allows for a structured decision-making support process when allocating limited financial and personnel resources to enhance preparedness and response to zoonotic diseases amplified by climate change.