We present a case of clear cell carcinoma located in the diaphragm in a patient with a medical history of ovarian endometriosis. Ultrasonography revealed the presence of a 2.5-cm nodule on the surface of the liver in a 65-year-old woman. She had undergone right salpingo-oophorectomy for treatment of an endometrial cyst of the right ovary at the age of 43 years and hysterectomy for treatment of a myoma of the uterus at the age of 51 years. We performed laparotomy and found that the tumor had originated from the diaphragm and invaded the liver. The diaphragm and liver were partially resected. Histopathological examination revealed the presence of clear cells and hobnail cells. The clear cells contained pale or eosinophilic cytoplasm and were arranged in a solid pattern. The hobnail cells lined the lumen and papillae. Immunohistochemical examination of the tumor cells showed positive staining for CK-7 and CA-125; negative staining for CK-20, TTF-1, and CA19-9; and weak positive staining for CEA. The findings were compatible with those of ovarian clear cell carcinoma. After 1 year, the patient had metastasis in the lung, and right lower lobectomy was performed.