Health benefits of physical activity in children are well known. However, a drawback is the risk of physical activity-related injuries. Children are at particular risk for these injuries, because of a high level of exposure. Because of the high prevalence of physical activity injuries and the negative short- and long-term consequences, prevention of these injuries in children is important. This article describes how we systematically developed a school-based physical activity injury prevention programme using the intervention mapping (IM) protocol. IM describes a process for developing theory- and evidence-based health promotion programmes. The development can be described in six steps: (i) perform a needs assessment; (ii) identify programme and performance objectives; (iii) select methods and strategies; (iv) develop programme; (v) adopt and implement; and (vi) evaluate. First, the results of the needs assessment showed the injury problem in children and the different risk factors for physical activity injuries. Based on the results of the needs assessment the main focus of the injury prevention programme was described. Second, the overall programme objective of the injury prevention programme was defined as reducing the incidence of lower extremity physical activity injuries. Third, theoretical methods and practical strategies were selected to accomplish a decrease in injury incidence. The theoretical methods used were active learning, providing cues and scenario-based risk information, and active processing of information. The practical strategy of the injury prevention programme was an 8-month course about injury prevention to be used in physical education classes in primary schools. Fourth, programme materials that were used in the injury prevention programme were developed, including newsletters for children and parents, posters, exercises to improve motor fitness, and an information website. Fifth, an implementation plan was designed in order to ensure that the prevention programme would be implemented, adopted and sustained over time. Finally, an evaluation plan was designed. The injury prevention programme is being evaluated in a cluster randomized controlled trial with more than 2200 children from 40 primary schools throughout the Netherlands. The IM process is a useful process for developing an injury prevention programme. Based on the steps of the IM we developed an 8-month injury prevention programme to be used in physical education classes of primary schools.