Although serious accidents remain the leading cause of pediatric mortality, protocols to orient diagnostic procedures towards a certain type of initial imaging are widely needed. Since 2007, we have performed whole-body magnetic resonance imaging (WBMR) and whole-body computed tomography (WBCT) for diagnoses of severely injured children. We retrospectively reviewed 134 WBMR and 158 WBCT in patients younger than 16 years that were performed at two trauma centers between 2007 and 2018. A higher Injury Severity Score (ISS) was found in WBCT vs. WBMR (10.6 vs. 5.8; p = 0.001), but without any significant difference in mortality. The WBMR was significantly preferred at younger ages (9.6 vs. 12.8 years; p < 0.001). The time between patient’s arrival until diagnosis was 2.5 times longer for WBCT (92.1 vs. 37.1 min; p < 0.001). More patients in the CT group received analgesic sedation and/or intubation at 37.3% vs. 21.6% in the MRI group. Of these patients, 86.4% (CT) and 27.6% (MRI) were already preclinically sedated (p < 0.001). Correspondingly, 72.4% of the patients were first sedated in-hospital for MRIs. In conclusion, WBMR is an alternative and radiation-free imaging method for high-energy-traumatized children. Although the selected diagnostics seemed appropriate, limitations regarding longer duration or additional analgesic sedation are present, and further studies are needed.