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Background: Intrasphenoidal encephalocele (ISE) is a rare clinical entity. The incidence of congenital encephalocele is very low. Accurate diagnosis and surgical approach is of critical value. Case Reports: We present a case of intrasphenoidal encephalocele in a 40-year-old man. He complained of cerebrospinal fluid (CSF) rhinorrhea and recurrent meningitis. In images of computed tomography (CT) and magnetic resonance imaging (MRI), intrasphenoidal encephalocele herniating through a defect of the left lateral sphenoid sinus wall was determined. Incisional biopsies were taken by endoscopic transnasal approach and histopathological examination revealed an encephalocele. In the differential diagnosis, ISE can be taken for inflammatory or malignant sinusoidal soft tissue masses. ISE is differentiated from other entities by demonstrating continuity with normal brain tissue. Conclusions: MRI clearly demonstrates that the herniating soft tissue is isointense with brain and continuous with brain tissue via the sphenoid sinus, thereby the treatment decision-making process is very important.