Klinefelter's syndrome is one of the most common forms of primary hypogonadism presenting with gynecomastia, azospennia and increased follicle-stimulating hormone. It is well known that this syndrome has an increased incidence of neoplasia, especially breast cancer and extragonadal germ cell tumors. However, it is rarely associated with an intracranial tumor of maldevelopmental origin, especially in the suprasellar area. We report, for the first time, a case of Klinefelter's syndrome, with a Rathke's cleft cyst is the patient was a 32-year-old male who was known to have an incidentaloma form brain computed tomography, which was clinically diagnosed as a suprasellar tumor. After operating, the suprasellar mass was confirmed as a Rathke's cleft cyst, and his hormonal abnormality, an elevated level of follicle-stimulating hormone, was not normalized. Therefore, we performed chromosomal analysis, and diagnosed Klinefelter's syndrome with the XXY karyotype.