The 46,XY disorder of sexual development (DSD) is a rare congenital condition characterized by a 46,XY karyotype associated with complete or disturbed female gonadal development and a non-virilized phenotype. The presence of Y chromosome material in these patients' karyotypes increases the risk of germ cell tumor development. The present study reports a unique case of a 16-year-old phenotypically female patient presenting with primary amenorrhea, who was later diagnosed with 46,XY DSD. After bilateral salpingo-oophorectomy, the patient was diagnosed with stage IIIC dysgerminoma. The patient received four cycles of chemotherapy and showed a good response. The patient is currently alive and well, with no evidence of disease after the residual lymph node resection.