Abstract Background Healthcare systems worldwide face challenges related to patient safety, quality of care, and interprofessional collaboration. Simulation-based team training has emerged as a promising approach to address some of these challenges by providing healthcare professionals with a controlled and safe environment to enhance their teamwork and communication skills. The purpose of this study protocol is to describe an intervention using simulation-based team training in pediatric departments. Methods Using a parallel-group, non-randomized controlled trial design, a simulation-based team training intervention will be implemented across four pediatric departments in Denmark. Another four pediatric departments will serve as controls. The intervention implies that healthcare professionals engage in simulation-based team training at a higher quantity and frequency than they did previously. Development of the intervention occurred from April 2022 to April 2023. Implementation of the intervention occurs from April 2023 to April 2024. Evaluation of the intervention is planned from April 2024 to April 2025. All simulation activity both before and during the intervention will be registered, making it possible to compare outcomes across time periods (before versus after) and across groups (intervention versus control). To evaluate the effects of the intervention, we will conduct four analyses. Analysis 1 investigates if simulation-based team training is related to sick leave among healthcare professionals. Analysis 2 explores if the simulation intervention has an impact on patient safety culture. Analysis 3 examines if simulation-based team training is associated with the treatment of critically ill newborns. Finally, Analysis 4 conducts a cost-benefit analysis, highlighting the potential return on investment. Discussion The implemented simulation-based team training intervention can be defined as a complex intervention. Following the Medical Research Council framework and guidelines, the intervention in this project encompasses feasibility assessment, planning of intervention, implementation of intervention, and rigorous data analysis. Furthermore, the project emphasizes practical considerations such as stakeholder collaboration, facilitator training, and equipment management. Trial registration Registered as a clinical trial on clinicaltrials.gov, with the identifier NCT06064045.