Pallister-Hall syndrome (PHS) is characterized by a spectrum of anomalies, which include polydactyly, hypothalamic hamartoma, laryngotracheal cleft, bifid epiglottis, imperforate anus, and renal abnormalities. Hypoplastic cochlea is a rare reported association of PHS. A baby girl was born at 31 weeks gestation with birth weight of 1.2 kg. The endotracheal intubation was extremely difficult due to narrow trachea. She was noted to be dysmorphic and have recurrent hypoglycemic episodes requiring high concentration of glucose infusion. The investigations revealed an inappropriately high plasma insulin and C-peptide level during hypoglycemia with low free fatty acids and β-hydroxy butyrate suggestive of congenital hyperinsulinism (CHI). MRI of the brain revealed the presence of a large hypothalamic hamartoma. The cochlea was noted to be truncated bilaterally with reduced number of turns. The cytogenetic analysis revealed GLI3 mutation consistent with diagnosis of PHS. This is the first reported case of CHI in association with PHS. Our patient also had hypoplastic cochlea, which is a unique but rarely reported feature of PHS.