Conventional intubation for pulmonary management in children with a difficult airway may be very challenging even in skilled hands. Rapid advancements in respiratory care have reduced the incidence of difficult tracheal intubation and the incidence of complications have decreased accordingly. However, serious unexpected complications still occur in some patients today. Herein, we describe a syndromic newborn infant with a difficult airway who experienced migration of the endotracheal tube into the esophagus after displacement of the tube connector. We would like to share our experience and contribute to the literature with the presentation of this undesired event. To the best of our knowledge, no such complication has been reported in the neonatal literature before.