Introduction: Glycine encephalopathy, also known as non-ketotic hyperglycinemia (NKH) represents a disorder characterized by elevated concentrations of glycine in all body tissues, especially in plasma and cerebrospinal fluids (CSF). NKH is caused by deficiency in the glycine cleavage system (GCS). Most glycine encephalopathy cases occur during the neonatal period. The current report presents a case of NKH neonatal intractable seizures. Evaluating a sick neonate who presents with hypotonia, encephalopathy, and seizures is a diagnostic challenge; a high index of suspicion for timely diagnosis and treatment could prevent severe complications. Case Presentation: The patient was a four-day-old baby girl in Iran admitted to the hospital due to hypotonia, lethargy and seizures. On the third day after discharge, the baby gradually lost the ability to suck milk and got sleepy and finally suffered from organ jump and seizures. Sepsis and antibiotics phenytoin tests were conducted and in metabolic testing, high level of glycine in blood and urine was reported and the patient was treated with sodium benzoate dextromethorphan and L-carnitine, after the start of the treatment, seizures and neurologic symptoms and alertness of the baby improved. The patient was discharged by continuing treatment after two weeks with seizure control, improved sucking reflexes and grasp. Conclusions: Since most of the symptoms of metabolic diseases in newborns are same as the signs of sepsis or other common diseases of this period, and also early diagnosis and treatment of these illnesses, especially in diseases such as hyperglycemia, can be influential in neural function of babies, it calls for serious attention and clinical vision of the doctors to stop mortality caused by such diseases by early consideration of serious complications.