Vallecular cyst is an uncommon but potentially dangerous condition causing stridor and has been associated with sudden airway obstruction resulting in death due to its anatomical location in neonates. It may also present with various degrees of feeding problems resulting in failure to thrive. When a vallecular cyst is suspected clinically, endoscopic laryngoscopy is necessary to visualize it. Other conditions leading to neonatal stridor such as laryngomalacia and other laryngotracheal abnormalities should be ruled out. Marsupialization with a CO₂ laser is the most effective and safest treatment to prevent recurrence. We report a case of a 1-month-old male infant with a vallecular cyst synchronous with gastroesophageal reflux, and failure to thrive. He was referred to our hospital because of hoarseness, inspiratory stridor, feeding-cyanosis, chest retraction and failure to thrive. Diagnostic workup revealed a cyst at the tongue base, suggesting a vallecular cyst. The cyst was removed by laryngomicrosurgery with CO₂ laser. After the surgery, the symptoms improved and the body weight increased steadily. We report a successfully treated case of neonatal vallecular cyst with symptoms of upper respiratory obstruction, gastroesophageal reflux, and failure to thrive.