Pyridox(am)ine- 5- phosphate Oxidase deficiency (PNPO) is a rare cause of neonatal metabolic encephalopathy associated with refractory status epilepticus. We report a case of a premature neonate presenting with drug-resistant seizures beginning at 2 hours of life. The baby showed initial transient response to pyridoxine followed by recurrence. Genetic report confirmed the diagnosis of PNPO deficiency. A literature review on phenotypic variants in terms of response to pyridoxine is also presented along with a proposed algorithm to manage a case of suspected vitamin responsive epilepsy. This case highlights our limited understanding of why variation in response to treatment exists in children with PNPO deficiency.