Objective To explore the clinical features of primary sphenoid sinus craniopharyngioma to improve the diagnose level and give the evidence for embryonic origin theory of tumorigenesis. Methods Clinical data 2 cases with primary sphenoid sinus craniopharyngioma was analyzed retrospectively, and relevant literature was reviewed. Results Of the 2 cases, the tumors were found occasionally with the symptoms of headache or orbital pain. The tyumor arose from sphenoid sinus, formed a cyst, presenting no homogeneous enhancement after contrast administration in MRI. Intraoperative detection showed the cyst contained yellow viscous liquid in both cases, and with cholesterol crystal in one. The symptoms relieved in both cases, no tumor recurred by 6 months followup postoperatively. Conclusion Primary sphenoid sinus craniopharyngiomas has been rarely reported in literature. It may originated in the residual cells of the cranial pharyngeal canal during the migration of Rathke’s pouch in embryonic period. This tumor must be differentiated from chronic sphenoid sinusitis and mucocele cyst. Pathological examination is the only way to confirm the diagnose of craniopharyngiomas. Complete surgical resection is the preferred method for the treatment of this tumor.