Mathematical modeling of infectious diseases is an important decision-making tool for outbreak control. However, in Africa, limited expertise reduces the use and impact of these tools on policy. Therefore, there is a need to build capacity in Africa for the use of mathematical modeling to inform policy. Here we describe our experience implementing a mathematical modeling training program for public health professionals in East Africa. We used a deliverable-driven and learning-by-doing model to introduce trainees to the mathematical modeling of infectious diseases. The training comprised two two-week in-person sessions and a practicum where trainees received intensive mentorship. Trainees evaluated the content and structure of the course at the end of each week, and this feedback informed the strategy for subsequent weeks. Out of 875 applications from 38 countries, we selected ten trainees from three countries - Rwanda (6), Kenya (2), and Uganda (2) - with guidance from an advisory committee. Nine trainees were based at government institutions and one at an academic organization. Participants gained skills in developing models to answer questions of interest and critically appraising modeling studies. At the end of the training, trainees prepared policy briefs summarizing their modeling study findings. These were presented at a dissemination event to policymakers, researchers, and program managers. All trainees indicated they would recommend the course to colleagues and rated the quality of the training with a median score of 9/10. Mathematical modeling training programs for public health professionals in Africa can be an effective tool for research capacity building and policy support to mitigate infectious disease burden and forecast resources. Overall, the course was successful, owing to a combination of factors, including institutional support, trainees' commitment, intensive mentorship, a diverse trainee pool, and regular evaluations.