An esophageal mucocele causing airway obstruction is an exceptionally rare complication of esophageal diversion in children. In this instance, they are fluid-filled dilatations of the esophageal remnant following bipolar exclusion of the thoracic esophagus. Only six pediatric cases have been reported previously in the literature. We present two consecutive cases of esophageal mucoceles causing respiratory distress in children following surgical exclusion of the esophagus. Bronchoscopy followed by imaging (computerized tomography or magnetic resonance imaging) was used to reach the diagnosis. Complete resection of the thoracic esophagus was required in both patients. Esophageal mucoceles can occur many years after esophageal exclusion, and the clinical features are often non-specific. Furthermore, complex co-morbidities may mask the underlying etiology of the respiratory distress, thus the diagnosis may be difficult to delineate. A high degree of suspicion, clinical awareness, and the use of the proper diagnostic tools, are essential for a diagnosis of mucoceles in children with a past history of esophageal exclusion.