Although chordomas are midline tumors, primarily intrasellar chordomas are extremely rare. In this report, the authors describe the case of a 68-year-old female with partial abducens nerve palsy in the right eye due to the intrasellar cystic tumor. After endonasal trans-sphenoidal surgery, intraoperative and histopathological findings confirmed the co-occurrence of an entirely intrasellar chordoma and pituitary adenoma. To our knowledge, the present case is the third reported case of an intrasellar chordoma with a pituitary adenoma.