The effects of climate change on infectious diseases are an important global health concern and necessitate decisions for allocation of resources. Economic tools have been used previously; however, how prioritization results might differ when done using broader considerations identified by local stakeholders has yet to be assessed. A multicriteria decision analysis (MCDA) approach was used to assess multi-stakeholder expressed concerns around disease prioritization via focus groups held in Quebec and Burkina Faso. Stakeholders weighted criteria and comparisons were made across study sites. A pilot disease prioritization was done to examine effects on disease rankings. A majority of identified criteria were common to both sites. The effect of context specific criteria and weights resulted in similar yet distinct prioritizations of diseases. The presence of consistent criteria between sites suggests that common concerns exist for prioritization; however, context-specific adjustments reveal much regarding resource availability, capacity and concerns that should be considered as this impacts disease ranking. Participatory decision aid approaches facilitate rich knowledge exchange and problem structuring. Furthermore, given multiple actors in low- and middle-income countries settings, multi-actor collaborations across non-governmental organizations, local government and community are important. Formal mechanisms such as MCDA provide means to foster consensus, shared awareness and collaboration.