Craniometaphyseal dysplasia is a rare congenital disorder that can cause craniofacial skeleton and tubular bone anomalies. A 7-month-old girl, with congenital facial palsy, mouth breathing, and nasal obstruction, was brought to the hospital because she suffered sudden cardiopulmonary arrest. Computed tomography showed bony narrowing of the choanae. The diagnosis was cardiopulmonary arrest triggered by asphyxia caused by severe choanal stenosis. She showed hypoxic encephalopathy and underwent a tracheotomy and an operation to enlarge choanae. When a neonate or young infant shows signs of nasal obstruction, physicians should aggressively search for and consider the possibility of choanal atresia or severe stenosis.