A 43-year-old male with sacral chordoma associated with rectal cancer is herein reported. A presacral tumor with extensive destruction of S4 and S5 was found 2.5 years after a low anterior resection for advanced rectal mucinous carcinoma. Under the preoperative diagnosis of a solitary sacral metastasis of rectal cancer, the lower sacral segments together with the tumor were removed by amputation at S3. Histologically, the tumor was a chordoma composed of polyhedral cells with an abundant eosinophilic cytoplasm mixed with typical vacuolated physaliferous cells within a myxoid matrix. Colorectal cancer associated with an extracolic primary malignant neoplasm is not uncommon; however, this is only the second case of colorectal cancer associated with chordoma to the best of our knowledge.