Chronic myeloid leukemia (CML) is a rare disease during childhood, and accelerated phase (AP) and blast phase (BP) CML, also called advanced phases, are even rarer. We retrospectively collected and analyzed clinical data of children younger than 20 years with de novo advanced-phase CML between 1996 and 2017 in Japan. Median follow-up time was 8.9 years for AP-CML (n = 15) and 3.7 years for BP-CML (n = 32). The 5-year overall survival (OS) was 93.3% for AP-CML, and 100.0% for patients who received tyrosine kinase inhibitors (TKIs) in first-line therapy (n = 10). Four of the ten patients who received TKIs in first-line therapy remained in molecular remission without transplantation (median follow-up 5.5 years). The 5-year OS of patients with BP-CML was 79.0%, and most patients received chemotherapy before transplantation, with regimen selection based on blast immunophenotype. Furthermore, among patients who received transplantation after TKI therapy, the 5-year OS was 100.0% for AP and 84.8% for BP. In conclusion, our study confirmed excellent outcomes in children with de novo advanced-phase CML, especially in the TKI-era.