Long-term data about the incidence of late adverse radiation effects (AREs) in pediatric brain arteriovenous malformations (AVMs) treated with Gamma Knife radiosurgery (GKRS) are lacking. This study addresses the incidence of late AREs, including cyst formation (CF), chronic encapsulated hematoma (CEH), and radiation-induced tumor, in pediatric patients with AVM treated with GKRS. This is a single-institutional study involving pediatric patients with AVM who underwent GKRS between 1991 and 2014. Among 201 pediatric patients with AVM (age ≤15 years), 189 who had at least 12 months of follow-up were assessed in this study. The median treatment volume was 2.2 cm3, and the median marginal dose was 20 Gy. The mean follow-up period was 136 months. During the follow-up period, symptomatic radiation-induced perilesional edema was found in 5 patients (3%), CFs in 7 patients (4%), CEHs in 7 patients (4%), and radiation-induced tumors in 2 patients (1%). The cumulative incidences of late AREs including CF, CEH, and radiation-induced tumor were 1.2% at 5 years, 5.2% at 8 years, 6.1% at 10 years, 7.2% at 15 years, and 17.0% at 20 years. In the multivariate analysis, treatment volume alone was a significant factor for late AREs (P < 0.001; hazard ratio, 1.111). GKRS is a reasonable treatment option for pediatric AVMs to prevent future intracranial hemorrhages, particularly in the eloquent regions. However, considerable attention should be paid to late AREs such as CFs, CEHs, and radiation-induced tumors because of longer life expectancy in pediatric patients.