Infectious disease modeling frameworks can offer decision support during infectious disease outbreaks. But the more complex a framework is, the less likely it is for it to come with an intuitive user interface–which is especially true for individual- or agent-based simulation frameworks. This limits accessibility and transparency for users with limited programming proficiency, impeding the utility for decision support. This paper describes a mixed-methods participatory design process of a graphical user interface (GUI) for the infectious disease modeling framework GEMS (German Epidemic Microsimulation System), as well as general insights for designing a GUI for complex decision-support systems. We involved current and potential users with varying levels of domain expertise all through the analysis of requirements and identification of use cases, the iterative development of the application and the final evaluation. The resulting web application is highly accessible even to modeling novices and facilitates the exploration of GEMS capabilities by running simple simulations. More generally, both technical constraints and differing user needs and capabilities makes a GUI for a modeling-based decision-support system more suitable for novice users than for experts, and for education and communication rather than for designing complex models. In balancing accessibility with functionality, one also needs to consider that each function requires extensive information and explanation, especially if the interface is designed for novice users. Future studies should explore how to extend the framework to best support exploration for different contexts, and for users with varying backgrounds.