Glial choristoma is considered to be a type of brain heterotopia consisting of ectopic central nervous tissue. We herein report a neonate with glial choristoma of the tongue who developed respiratory distress due to airway obstruction. A male neonate presented with respiratory distress due to a soft mass on the midline region of the dorsal tongue base at birth. He was intubated using a flexible fiberoptic nasopharyngoscope. MRI showed a well-circumscribed mass measuring 25 × 23 × 27 mm in size in the same region. A histologic examination confirmed a pathological diagnosis of glial choristoma. He underwent tracheotomy at 22 days of age, and a subtotal resection of the tumor was performed at five months of age. The clinical behavior of oral glial choristoma varies depending on the age at onset as well as the location and size of the mass. The small size of the organ and the narrow operating field hamper the surgical approach in neonates. The optimal therapeutic strategy for neonatal cases of glial choristoma should thus be determined based on the condition of each individual patient.