Persisting embryonal infundibular recess (PEIR) is a rare anomaly of the third ventricular floor. Only eight cases have been published. In this report, a case of presumably Rathke’s cleft cyst associated with cerebrospinal fluid leakage caused by PEIR is described. An 81-year-old woman underwent endoscopic transsphenoidal surgery for the intra- and supra-sellar cystic lesion. Intraoperatively a hole was confirmed over the sella turcica connecting the sellar cyst and the infundibular recess. Liquorrhea did not occur throughout the procedure. A computed tomography (CT) scan obtained immediately after surgery disclosed accumulation of air in the third and lateral ventricles, in addition to the intra- and supra-sellar region. Air accumulation resolved spontaneously after bed rest for 11 days and she was discharged without neurological deficits. However, she required the second transsphenoidal surgery to repair the sellar floor because of bacterial meningitis caused by liquorrhea on the postoperative day 23. A postoperative 3-tesla magnetic resonance image revealed a deep infundibular recess connecting the sella turcica and the third ventricle, which was considered to be PEIR. To the best our knowledge, this is the first reported case describing the intraoperative findings of PEIR.