CHARGE syndrome is a multiple congenital anomaly syndrome that can be life-threatening in the neonatal period. Complex heart defects, bilateral choanal atresia, esophageal atresia, severe T-cell deficiency, and brain anomalies can cause neonatal death. As little is known about the causes of death in childhood and adolescence, we studied post-neonatal death in patients with CHARGE syndrome. We collected medical data on three deceased children from a follow-up cohort of 48 CHARGE patients and retrospectively on an additional four deceased patients (age at death 11 months to 22 years). We analyzed the factors that had contributed to their death. In five patients respiratory aspiration had most likely contributed to premature death, one died of post-operative complications, and another choked during eating. From our findings and a literature review, we suggest that swallowing problems, gastro-esophageal reflux disease, respiratory aspiration and post-operative airway events are important contributors to post-neonatal death in CHARGE syndrome. Cranial nerve dysfunction is proposed as the underlying pathogenic mechanism. We recommend every CHARGE patient with feeding difficulties to be assessed by a multidisciplinary team to evaluate cranial nerve function and swallowing. Timely treatment of swallowing problems and gastro-esophageal reflux disease is important. Surgical procedures on these patients should be combined whenever possible because of their increased risk of post-operative complications and intubation problems. Finally, we recommend performing autopsy in deceased CHARGE patients in order to gain more insight into causes of death.