Conventional radiation therapy for small children with malignant brain tumors might elongate the lifetime but causes severe chronic neurocognitive effects and functional deficits. Boron neutron capture therapy (BNCT) can selectively destroy tumor cells with little damage to normal brain tissue, which promises good quality of life. We studied the clinical outcomes and courses in patients under 18 years old with malignant brain tumors. Among 183 patients with brain tumors treated by our group using BSH-based intraoperative BNCT, 29 patients were under 18 years. They included 11 patients less than 5 years. There were four glioblastomas (GBM), nine anaplastic astrocytoma (AAS), and seven primitive neuroectodermal tumors (PNET). Six patients had pontine gliomas, and one had anaplastic ependymoma. Seven out of 29 patients have lived more than 10 years and we followed five patients for more than 20 years after BNCT. Radiation necrosis was observed in only one patient, who suffered from hemiparesis and neurocognitive sequelae. The other patients had little damage caused by BNCT. BNCT can be applied to malignant brain tumors in children, especially those under 3 or 5 years of age, instead of conventional radiation therapy.