Cryptorchidism, or undescended testes, is a common congenital condition that significantly increases the risk of testicular malignancy, particularly germ cell tumors (GCTs), with a higher risk in the left testis. Persistent Müllerian Duct Syndrome (PMDS) is a rare disorder in males, where Müllerian structures such as a uterus or fallopian tubes are present despite the individual having a Y chromosome and male external genitalia. The concurrent occurrence of cryptorchidism, testicular tumors, and PMDS is extremely rare, making this case noteworthy. We report the case of a 24-year-old male with a history of bilateral cryptorchidism, who presented with an abdominal mass and intermittent pain. Imaging studies revealed a complex mass suggestive of a testicular tumor. During surgery, a small structure resembling a uterus was discovered and excised alongside both undescended testes. Histopathological evaluation confirmed a mixed GCT consisting of yolk sac tumor, seminoma, and teratoma arising from the undescended left testis. Additionally, the incidental finding of a uterine-like structure was consistent with PMDS. Postoperatively, the patient recovered without complications, with tumor markers normalizing within one month. Follow-up imaging and physical exams showed no recurrence at six months. This case highlights the rare association of PMDS with cryptorchidism and testicular tumors, emphasizing the importance of a multidisciplinary approach to diagnosis, treatment, and genetic counseling, particularly regarding fertility and associated conditions.