Best practices in wildlife disease management require robust evolutionary ecological research (EER). This means not only basing management decisions on evolutionarily sound reasoning, but also conducting management in a way that actively contributes to the on-going development of that research. Because good management requires good science, and good science is ‘good’ science (i.e., effective science is often science conducted ethically), good management therefore also requires practices that accord with sound ethical reasoning. To that end, we propose a two-part framework to assist decision makers to identify ethical pitfalls of wildlife disease management. The first part consists of six values – freedom, fairness, well-being, replacement, reduction, and refinement; these values, developed for the ethical evaluation of EER practices, are also well suited for evaluating the ethics of wildlife disease management. The second part consists of a decision tree to help identify the ethically salient dimensions of wildlife disease management and to guide managers toward ethically responsible practices in complex situations. While ethical reasoning cannot be used to deduce from first principles what practices should be undertaken in every given set of circumstances, it can establish parameters that bound what sorts of practices will be acceptable or unacceptable in certain types of scenarios.