Nasopharyngeal encephalocele is a rare, benign congenital anomaly. It has the potential to be fatal due to airway obstruction. Here, we report on a 34-day-old infant with pneumonia who underwent mechanical ventilation. An upper airway evaluation was performed due to prolonged intubation, and revealed the presence of a nasopharyngeal encephalocele. The patient tolerated extubation and oral feeding after surgical resection of the lesion. Awareness of the condition can help clinicians arrive at an earlier diagnosis and enhance management.