Hyperprolinemia type II (HP II) is a rare inherited metabolic disease due to the deficiency of pyroline-5-carboxylate dehydrogenase. It is generally believed to be a benign condition although some patients have neurological problems such as refractory convulsions. Here we report a six-year-old girl with HP II who admitted to our hospital with recurrent seizure refractory to multiple antiepileptic drugs. She was the third child of healthy, consanguineous parents. The family history was negative for neurological and renal disorders. On physical examination, she had no facial dysmorphy; the anthropometric measurements, and systemic and neurological examinations were normal. Mental and motor development was appropriate for her age. Laboratory findings revealed elevated levels of proline, glycine, and ornithine in serum and pyrroline-5-carboxylate and hydroxyproline in urine. Cerebral computerized tomography and magnetic resonance imaging were both normal. Electroencephalogram showed a very active epileptic abnormality; partial control of seizures was achieved by two antiepileptics. Increased plasma glycine and ornithine levels are the unique features of our case when compared to the other HP II cases reported in the literature.