VACTERL association is linked to multiple congenital anomalies including tracheoesophageal fistula. In rare cases, VACTERL has been complicated by other airway malformations including severe bronchial stenosis or unilateral pulmonary agenesis. We report a child who developed episodes of oxygen desaturation during sleep associated with high pressure support requirements to maintain ventilation. He was known to have VACTERL association as well as spinal muscular atrophy (SMA) type II, a genetic neuromuscular disorder. Children with SMA can show progressive respiratory symptoms, including intercostal muscle weakness and accompanying paradoxical abdominal breathing with sparing of diaphragm function. Our patient was very difficult to ventilate non-invasively despite high pressures. CT chest with dynamic airway evaluation showed bilateral bronchial stenosis. High inspiratory pressures with non-invasive ventilation as seen in our case are required to overcome stenotic airways but are not expected in neuromuscular respiratory failure.