Recent progress in the treatment for pediatric malignancies using a combination of surgery, chemotherapy, and radiotherapy has improved survival. However, late toxicities of radiotherapy are a concern in long-term survivors. A recent study suggested reduced secondary cancer and other late toxicities after proton beam therapy (PBT) due to dosimetric advantages. In this study, we evaluated the safety and efficacy of PBT for pediatric patients treated in Japan. A retrospective observational study in pediatric patients who received PBT was performed. All patients aged <20 years old who underwent PBT from January 1983 to August 2014 at four sites in Japan were enrolled in the study. There were 343 patients in the study. The median follow-up periods were 22.6 months (0.4-374.3 months) for all patients and 30.6 months (0.6-374.3 months) for survivors. The estimated 1- ,3- , 5- , and 10-year survival rates were 82.7% (95% CI: 78.5-87.0%), 67.4% (61.7-73.2%), 61.4% (54.8-67.9%), and 58.7% (51.5-65.9%), respectively. Fifty-two events of toxicity >= grade 2 occurred in 43 patients. Grade 4 toxicities of myelitis, visual loss (two cases), cerebral vascular disease, and tissue necrosis occurred in five patients. This study provides preliminary results for PBT in pediatric patients in Japan. More experience and follow-up with this technique are required to establish the efficacy of PBT in this patient population.