A major complication of retained testes is an occurrence of malignancy later in life. We, herein, report the case of a 2-year-old boy who presented with a huge yolk sac tumor with retroperitoneal lymph nodes metastasis that originated in a left intra-abdominal undescended testis. Computed tomography and magnetic resonance imaging showed a huge round tumor connecting to the left retroperitoneal lymph nodes with metastasis extending from the left pelvic region to the left renal hilum. The serum alpha-fetoprotein level was 36,528 ng/mL. The right abdominal tumor appeared to be a giant testis that had strangulated at the neck of the cord. The tumor had ruptured at the side of the left pelvic lymph node metastasis, and a yolk sac tumor was diagnosed from a histologic analysis of the resected specimens. Postoperative PEB chemotherapy was effective, and a complete surgical resection of the tumor was performed 3 months after the initial laparotomy. The pathologic findings showed fibrous tissue without any tumor cells. The patient has been doing well for 18 months after the radical operation. This case might be a coincidental association of a yolk sac tumor occurring in an undescended testis, which thus caused a delay in making an accurate diagnosis.