Limited information is available on the design of combined innovation and entrepreneurship training courses, and with even less available on delivering such courses to multidisciplinary teams. We designed an extracurricular project-based training course in innovation and entrepreneurship and delivered it to transdisciplinary teams of students who were then asked to build an autonomous mobile system for healthcare applications and to create a business model to implement it. The course was created through a backward educational design and design thinking to assist teams of students in transforming an idea into a technical solution and developing it into a business model through a project-based learning experience. A transdisciplinary group of 31 students, mostly in bachelor’s degree programs, worked either all together, in plenary sessions, in subject-specific groups, or in teams of 5–6 members, under the guidance of their trainers during a ten-day summer school. We used questionnaires to evaluate the changes in student perceptions and a satisfaction survey to evaluate the students’ experience. The qualitative observations together with the results of the quantitative instruments revealed positive changes in student perceptions towards innovation and entrepreneurship. Additionally, the satisfaction survey offered positive feedback and some recommendations for further improvement. The implementation of the course showed that planning is important, but flexibility is essential, that covering fewer topics might lead to deeper understanding, and that managing expectations and practicing empathy are crucial.