An 11-year-old boy with Lowe syndrome developed secondary sexual characteristics within a few weeks, suggestive of precocious puberty. His blood tests were positive for serum-human chorionic gonadotropin, and imaging revealed a right thymic lobe mass containing small cystic lesions. A germ cell tumor with malignant potential was suspected. Thus, we performed an extended thymectomy with mediastinal lymph node dissection and confirmed germinoma of the right thymic lobe without lymph node metastasis; the patient underwent four courses of chemotherapy. Follow-up evaluations indicated no recurrence. Thus, we present a highly rare case report of thymic germinoma complicated by Lowe syndrome.