Several central nervous system complications in pediatric patients with hematological malignancies have been reported. We analyzed the frequency and the correlation with central nervous system involvement and intrathecal therapy. The frequency was 13 % (11/85), being almost equal to those in literature. We investigated high intensity areas, which indicated leukoencephalopathy, in the white matter by T2-weighted and/or fluid attenuated inversion recovery images (FLAIR) of the brain magnetic resonance imaging (MRI). Incidence of white matter lesions was higher in patients who received over 10 times of intrathecal therapy (p = 0.018). Patients who received repetitive intrathecal therapy should undergo close MRI to find out if they need cognitive functioning test. However, it may be possible to omit brain MRI in patients with acute myeloid leukemia and lymphoma who have received intrathecal therapies less than five times in a consideration of their burden in terms of sedation and cost.