We report a 43-year-old male-to-female transsexual patient with gender identity disorder (GID), suffering from neurovascular compression causing glossopharyngeal and vagal nerve palsy. Cross-sex hormone therapy has been approved for 5 years. He had complained of difficulty inn speaking and singing for 3 years, with symptoms of right soft palate palsy, lower sensitivity of the right pharynx and curtain sign. However, recurrent nerve palsy was not identified so his vocal cord mobility was good. We investigated brain MRI and MRA, and detected dolichoectasia of the right vertebral artery on the medulla. We suspected that the neural symptoms on the same side were caused by the vertebral artery dolichoectasia compressing his glossopharyngeal and vagal nerve on the medulla.