The development of multiple organ failure and septic complications increases the cumulative risk of mortality in children with severe injury. Clinically available biochemical markers have shown promise in assessing the severity and predicting the development of complications and outcomes in such cases. This study aimed to determine informative criteria for assessing the severity and outcome prediction of severe injury in children based on levels of mid-regional proadrenomedullin (MR-proADM) procalcitonin (PCT), neuron-specific enolase (NSE), and protein S100. Biomarker levels were measured in 52 children with severe injury (ISS ≥ 16) on the 1st, 3rd, 7th, and 14th days after admission to the ICU. The children were divided into groups based on their favorable (n = 44) or unfavorable (n = 8) outcomes according to the Severe Injury Outcome Scale, as well as their favorable (n = 35) or unfavorable (n = 15) outcomes according to the Glasgow Coma Outcome Scale (GOS). The study also evaluated the significance of biomarker levels in predicting septic complications (with SC (n = 16) and without SC (n = 36)) and diagnosing and stratifying multiple organ failure (with MOF (n = 8) and without MOF (n = 44)). A comprehensive assessment of MR-proADM and PCT provided the highest diagnostic and prognostic efficacy for early diagnosis, risk stratification of multiple organ failure, and outcome prediction in severe injury cases involving children. Additionally, the inclusion of the S100 protein in the study allowed for further assessment of brain damage in cases of traumatic brain injury (TBI), contributing to the overall prognostic model.