Neonatal nonketotic hyperglycinemia (NKH) is an extremely rare disease that causes intractable seizures and severe psychomotor retardation. Currently, effective treatment for NKH has not yet been established. Here we report a boy who exhibited intractable seizures at 7 days old. EEG revealed supression burst pttern, followed by hypsarrythmia at 5 months old. Patient’s symtom was completely resistent to many kinds of anti-epileptic drugs including phenobarbital and VitB6 therapy. Thus, we measured the glycine concentration of ceberal flued of the patient, which led to the final diagnosis of the patient as NKH. Ketogenic diet therapy was started, which improved his EEG findings. Moreover, subsequent zonisamide treatemnt was apparently effective for the seizures. In conclusion, we propose that ketogenic diet and zonisamide could be effective in the treatment of NKH.