Introduction Hyperinsulinism is the most common cause of both transient and persistent hypoglycemia in the neonatal period. Hyperinsulinism due to mutations in the ATP-sensitive potassium channel encoded by the KCNJ11 and ABCC8 genes cause the most common and severe form of hyperinsulinism. Herein, we present a case of congenital hyperinsulinism in which a novel KCNJ11 mutation was identified. Case report An eight-day-old boy with a birth weight of 4,550 g born to a 32-year-old female with diabetes mellitus was transferred to our clinic with the diagnoses of respiratory distress syndrome, congenital heart disease and hypoglycemia. A diagnosis of congenital hyperinsulinism was made based on the presence of elevated serum insulin levels (109 mu IU/mL [2.6-24]) during hypoglycemia. Levels of serum growth hormone, cortisol, ammonium, and lactate were normal. Metabolic screening tests for blood and urine ketones and fatty acid oxidation defects were found to be normal. Glucose infusion (14 mg/kg/min), glucagon infusion, and diazoxide were initiated based on the diagnosis of hyperinsulinemic hypoglycemia; however, glycemic control was only achieved after the addition of octreotide and nifedipine. There were no abnormal findings in sonography and abdominal magnetic resonance imaging. Molecular diagnosis ABCC8 and KCNJ11 mutation analyses was performed on the genomic DNA extracted from peripheral blood. A novel homozygous missense mutation (p.E126K) was detected in KCNJ11 confirming the diagnosis of congenital hyperinsulinism. Conclusion A novel homozygous missense mutation (p.E126K) was detected in our case, which resulted in hyperinsulinism.