A 14-year-old boy presented with regurgitation, malnutrition, and chronic lung insufficiency with a history of successful repair of esophageal atresia and tracheoesophageal fistula in the newborn period. Barium swallow and manometry results showed achalasia. Hellar operation with antireflux procedure resulted in complete symptomatic relief. Histology and immunohistochemistry including PGP9.5, MAP5, cKit, and nNOS of myotomy specimen showed intact innervation. Although esophageal dysmotility after esophageal atresia repair usually is caused by gastroesophageal reflux and incoordination of peristalsis, the possibility of achalasia should also be considered, because a casual relationship between esophageal atresia and achalasia may exist.