Some neonatal hypoglycemias have genetic origins. For instance, mutation in forkhead box protein A2 (FOXA2), located on chromosome 20p11.21, has recently been reported to cause hyperinsulinemic hypoglycemia and hypopituitarism. Here, we report a case of hyperinsulinemic hypoglycemia and GH deficiency (GHD) with 20p11.23-p11.21 deletion, which included FOXA2. The boy was diagnosed with hyperinsulinemic hypoglycemia during the neonatal period and subsequently administered diazoxide for treatment. His blood glucose levels gradually stabilized, and the diazoxide dosage was slowly reduced and ultimately fully weaned. The patient was discharged at the age of 29 d. Unfortunately, the patient experienced recurrent hypoglycemia at 3 mo, and diazoxide administration was re-initiated. Further examination, including chromosomal microarray analysis, revealed a 2.48-Mb 20p11.23-p11.21 deletion that encompassed FOXA2. In addition, severe GHD was detected, and magnetic resonance imaging of the brain revealed pituitary stalk interruption. Accordingly, GH replacement therapy was started at 0.175 mg/kg/wk, and blood glucose levels were stabilized. Our report suggests that there are pathological conditions that can cause both hyperinsulinemic hypoglycemia and hypopituitarism and reaffirms the importance of evaluating not only insulin and congenital metabolic disorders but also pituitary function in patients with hypoglycemia.