Computing education is becoming increasingly important in high school curricula, but there are challenges in teaching computing, including teachers’ professional development and the development of appropriate learning tools. Participatory design and cooperative prototyping offer opportunities for identifying challenges in computing education and a way for teachers to be involved in the design of learning tools in the form of prototypes. This study describes the process of co-designing a learning tool to overcome some of these challenges for computing education in high school with teachers, developers, and researchers as collaborators. The study investigating how cooperative prototyping and participatory design can lead to mutual learning about challenges in teaching computing. Prototypes of a learning tool, CoTinker, were developed in collaboration between six teachers, two developers, and four researchers in four subcases and implemented in classrooms with a total of 83 students. Challenges such as students’ collaboration and transfer of knowledge in computing education were overcome by applying the prototypes in computing education classrooms in high school. We suggest that participatory design and cooperative prototyping with a group of teachers offers ways to identify and address challenges in computing education and to develop learning tools for them.