Pyridoxal 5'-phosphate (PLP)-responsive epilepsy is a rare autosomal recessive epileptic disorder caused by deficiency of pyridox(am)-ne 5'-phosphate oxidase (PNPO). Neonatal onset seizures in PLP responsive epilepsy are usually resistant to common anticonvulsants and pyridoxine, but respond to PLP. Various PNPO mutations are associated with this disorder. In this report, we have described a case of a female baby with neonatal onset seizures responding to PLP. Exome sequencing revealed that the patient was compound heterozygous for pathogenic mutations [c.546+1G>A (IVS5+1 G>A) and c.620delG (p.G207VfsX215)] in the PNPO gene. The c.546+1G>A was inherited from the mother while the c.620delG was inherited from the father. Both mutations were absent in 122 unrelated Thai controls. The results of this study indicated the presence of two newly identified mutations in this Thai patient with PLP-responsive epilepsy for the first time, expanding the mutational spectrum of PNPO.