Background: The clinical presentation of sphenoid sinus meningoencephaloceles (MEC) may have insidious onset and evolution. Contemporary treatment incorporates endoscopic resection via the endonasal route. Case description: We present a case of 3 year old girl who had been complaining of permanent nasal discharge, impeded nasal breathing and difficulty with feeding since she was 5 months old. There was no history of rhinoliquorrhea. Pre-operative magnetic resonance imaging demonstrated MEC that extended from the sellar region through the non-pneumatized sphenoid sinus to the nasopharynx. The lesion was resected via endoscopic endonasal approach. Follow-up rhinoscopy confirmed the absence of post-operative cerebrospinal fluid leak. Conclusion: Endoscopic endonasal approach can be an effective and a safe treatment option for resection of congenital transsphenoidal MEC in early childhood.