Project-based learning can increase student engagement, making an undergraduate course more like an independent research experience. In semester-long projects, students develop mathematical models for a disease of their choice, and use those models to investigate a research question with numerical simulations in the software R. Unlike a ‘wet lab’ setting, using mathematical models means that students can research a broad range of diseases, even virulent human pathogens. This can further increase engagement, particularly for pre-health students. Through their work on the project, students reinforce foundational disease ecology concepts, practice using mathematical models as experimental tools, and develop computational skills.