Background To evaluate the therapeutic benefits and side effects (especially leukoencephalopathy) of intrathecal methotrexate (MTX) in children aged over three years old with high-risk medulloblastoma (MB). Methods In the present retrospective study, patients who received intrathecal MTX during chemotherapy were classified as MTX group, while those receiving cerebrospinal fluid (CSF) cytology analysis only were recruited in control group. Results Among the 46 MB patients, 32 were classified in MTX group, whereas 14 in control group. For those 32 patients in MTX group, 27 (84.38%) had metastatic disease, 3 (9.38%) had diffuse anaplasia, and 3 (9.38%) had residual disease greater than 1.5 cm ². Molecular subgroup classification was available in 28 (87.5%) patients. Of those 14 patients in control group, 8 (57.14%) had metastatic disease, 3 (27.27%) had diffuse anaplasia, and 6 (42.86%) had residual disease greater than 1.5 cm ². Molecular subgroup classification was available in 6 (42.86%) patients. The 5-year progression-free survival (PFS) was 70.99% (95% CI, 58.22%-90.42%) and 5-year overall survival (OS) was 72.99% (95% CI, 60.41%-93.06%) for MTX group, while those were 41.67% (95% CI, 17.93%-66.92%) and 50% (95% CI, 27.88%-77.14%) for control group, separately. Among the 32 patients in MTX group, 6 (18.75%) with group 4 disease developed MTX-related acute leukoencephalopathy and one of them died. Conclusions Intrathecal MTX improves the 5-year PFS and OS for children with high-risk MB. However, intrathecal MTX is not recommended for patients with group 4 MB due to the high risk of acute leukoencephalopathy.