Inter-hospital transfers of severely injured patients are inevitable due to limited resources. We investigated the association between inter-hospital transfer and the prognosis of pediatric injury using the Korean multi-institutional injury registry. This retrospective observational study was conducted from January 2013 to December 2017; data for hospitalized subjects aged < 18 years were extracted from the Emergency Department-based Injury in Depth Surveillance database, in which 22 hospitals are participating as of 2022. The survival rates of the direct transfer group and the inter-hospital transfer group were compared, and risk factors affecting 30-day mortality and 72- hour mortality were analyzed. The total number of study subjects was 18,518, and the transfer rate between hospitals was 14.5%. The overall mortality rate was 2.3% (n = 422), the 72-hour mortality was 1.7% (n = 315) and the 30-day mortality rate was 2.2% (n = 407). The Kaplan-Meier survival curve revealed a lower survival rate in the inter-hospital transfer group than in the direct visit group (log-rank, < 0.001). Cox proportional hazards regression analysis showed that inter-hospital transfer group had a higher 30-day mortality rate and 72-hour mortality (hazard ratio HR, 1.681; 95% confidence interval CI, 1.232-2.294 and HR, 1.951; 95% CI, 1.299-2.930) than direct visit group when adjusting for age, sex, injury severity, and head injury. Among the pediatric injured patients requiring hospitalization, inter-hospital transfer in the emergency department was associated with the 30-day mortality rate and 72-hour mortality rate in Korea.