Background: 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. Methods: 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 interhospital transfer group were compared, and risk factors affecting 30-day mortality and 72-hour mortality were analyzed. Results: 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, P < 0.001). Cox proportional hazards regression analysis showed that interhospital 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. Conclusion 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.