We reported a case of Rathke's cleft cyst (RCC) with a moving mass in the cyst. A fifty-eight-year-old woman complaining of headache was admitted to our hospital. She suffered from hyponatremia, hypothalamic hypopituitarism, but did not show any neurological deficits, nor visual field nor visual acuity disturbance. MRI revealed an intrasellar cyst including a mass shadow and the cyst did not compress the hypothalamus. Interestingly, this mass moved gradually from the floor to the posterior wall of the sella turcica according to changes in position from standing to supine. We operated to remove the cyst partially by transsphenoidal approach. Xanthochromic fluid flowed out from the cyst. In addition, a brownish globular mass, 6 mm in diameter, existed within the cyst without connection to the surrounding tissue. Pathological findings showed that the capsule consisted of cuboid epithelium and was partially stratified, which confirmed the diagnosis of Rathke's cleft cyst. However, the mass was homogeneously stained with H.E., containing no cells, cellular debris, nor connective tissue. PAS stain was negative. Though we could not clarify the material in the cyst, this case is very rarely one of Rathke's cleft cyst. This case demonstrated the possibility of hypothalamic hypopituitarism in spite of the cyst being almost located in the sella turcica. We surmise that a cyst near the stalk of the pituitary gland, even if it is not so large, might compress the portal vein, and thus the function of hypothalamus-pituitary axis.