Mobile health applications can help to disseminate educational health interventions and be widely used. However, mobile health applications not carefully developed will likely not be adopted by the intended users. This paper describes the methodology used to develop a mobile health application for teaching critical thinking about health to youth attending youth friendly centres in Rwanda. The app includes the adapted content of a children’s “health choices book”. We adapted the book into audio podcasts to fit the context of young adults. The application was developed following a framework for developing mobile health applications. The framework follows three theories: health belief model, the theory of planned behavior and technology acceptance model. We developed an Android based application which can be freely accessed in the Play store. The content in the app explains the need for critical thinking, the 10 audio podcasts, the support, and chat window where users share their experience of using the app. The app will be piloted in two youth centers in Rwanda.