Posterior glottal stenosis (PGS) is a potentially life-threatening condition associated with bilateral vocal fold immobility (BVFI) that is often difficult to diagnose and treat. We herein report a case of PGS with malformation of the arytenoid cartilage that was successfully treated with arytenoidectomy. The patient was a 20-year-old woman, who had been a very low birth weight infant. She developed pneumonia immediately after birth and underwent prolonged intubation and tracheostomy. She had been diagnosed with BVFI at a previous hospital. As she had no symptoms, the tracheostomy was closed at 19 years of age. However, one year and six months later, she developed inspiratory stridor and hoarseness, and was referred to our hospital. Fiberoptic laryngoscopy and CT tomography revealed suspected PGS. Under general anesthesia, direct laryngoscopy revealed malformation of the right arytenoid cartilage deflecting in the anteromedial direction and excessive anterior mucosa covering the posterior glottis, which led to a diagnosis of PGS. A traction test of the arytenoid cartilage indicated right vocal fold fixation. Subsequently, resection of the anterior excessive mucosa and part of the arytenoid cartilage was performed to widen the posterior glottis by performing laryngomicrosurgery. Postoperatively, her voice and respiratory symptoms improved. For a definite diagnosis of PGS, it is important to confirm the presence of organic lesions in the posterior glottis and the passive movement of bilateral arytenoids under direct laryngoscopy. Surgical treatment for PGS should be performed based on the pathophysiological conditions.