The aim of the study was to explore the association between Glasgow Coma Scale (GCS), Paediatric Index of Mortality (PIM2) and Injury Severity Score (ISS), and the long-term outcome of children with injuries. The health related quality of life (HRQL) was assessed by using the Royal Alexandra Hospital for children Measure of Function (RAHC MOF), 12 months post discharge. Out of 118 children with injuries (9% of all patients), 75 had injury of the head as the leading injury. There were no significant differences at admission in the severity of clinical condition, as expressed by PIM2 and ISS, between patients with head injuries and patients with other injured leading body regions. Children with head injuries had significantly worse HRQOL than children with other leading injured body region (p < 0.045), and children from road traffic accidents had significantly worse HRQL (p = 0.004), compared to other mechanisms of injury. HRQL correlated significantly with GCS (p = 0.027), but not with ISS and PIM2. As the conclusion, among all scoring systems applied, only GCS, which demonstrates severity of head injury, showed significant impact on long-term outcome of injured children.