There are some kinds of neoplasms to be differentiated in the clival area, such as chordoma, invasive pituitary adenoma, craniopharyngioma, trigeminal neuroma, epidermoid cyst, and epidermoid tumor. A 12-year-old girl had admitted with a chief complaint of diplopia. On computed tomography and magnetic resonance(MR) image , cystic mass of about 4cm in diameter which partially destroyed bony structure at posterior part of the clivus was compressing brainstem slightly at anterior direction. This mass showed hyperintensity on T2-weighted MR image, hypointensity on T1-weighted MR image and especially hyperintensity on diffusion image, but no contrast enhancement. So, We suspected a epidermoid cyst and planned biopsy through a transsphenoidal approach. Fortunately, tumor was removed completely. This tumor was considered as epidermoid cyst on MR image. But, it was confirmed as chordoma in pathologic diagnosis. Therefore, we report this case and it may be helpful to make a differential diagnosis in clival cystic chordoma preoperatively that has multilobulation, bony erosion, and calcification on radiologic findings.