This paper relates a capstone design project conceived through an engineering problem-based learning approach. The project is applied to critical embedded systems and the Scrum Agile method is used. The focus of the paper is on the pedagogical experience, so the Intended Learning Outcomes and pedagogical sequence over one semester are presented. Two platforms (the Parrot AR.Drone 2 and a toy car) were used for the project. Pros and cons of such platforms are debated. Tools like Git for the version control and iceScrum for the Agile management are presented. The different roles of teachers as clients, counselors, and evaluators are detailed. This paper shows that an interdisciplinary teaching team is very important in this kind of project, so is the teachers’ engagement in the Agile philosophy. Feedback, analyses and some suggested improvements are given, based on our 5 years’ experience in such projects and surveys.