We excised a bronchogenic cyst causing recurrent laryngeal nerve palsy using thoracoscopic surgery. A 28-year-old woman presented after the sudden onset of hoarseness, and laryngoscopic examination showed left vocal cord palsy. Computed tomography and magnetic resonance imaging showed a cystic mass, 4 cm in diameter, in the aortopulmonary window. Thoracoscopic examination revealed that the mass was adhered to the recurrent laryngeal nerve below the aortic arch. We extirpated the cyst via thoracoscopy without any injury to the nerves or major blood vessels. This case illustrates the benefits of thoracoscopic surgery for providing good visualization of the perineural structures and as a safe surgical treatment for a cystic mass in the aortopulmonary window.