Neither accurate incidence nor survival data for pediatric patients with hematological malignancies (HM) have been available in Japan to date. Incidence of patients under 20 years of age, who were diagnosed with HM from 2006 to 2010, and their two-year survival rate (2y-OS) were obtained from disease registry data maintained by the Japan Society of Pediatric Hematology (JSPH). A total of 5,287 cases of HM were identified during this period. Acute lymphoblastic leukemia (ALL, 46.6%) showed the highest incidence, followed by acute myeloid leukemia (AML, 16.7%), non-Hodgkin lymphoma (NHL, 11.9%), and histiocytosis (11.8%). ALL, AML and histiocytosis were common in younger patients aged 1-4, while NHL tended to occur more frequently in older patients aged 5-14. The 2y-OS of HM was 91.6%, with that for the most common B-precursor ALL rising to 96.2%. The 2y-OS for M3 AML, lymphoblastic-B-precursor or diffuse large B cell NHL, Hodgkin lymphoma, myeloproliferative disorders, and Langerhans cell histiocytosis was >95%. There were no gender differences in prognosis, while infants (88.0%) and adolescents aged 15-19 (90.6%) tended toward a poorer prognosis. This is the first report to describe incidence and survival times from the nationwide JSPH disease registry. More precise data with longer follow-up is needed.