The formation of an intracranial abscess secondary to sphenoid sinus occlusion after nasoseptal flap skull base reconstruction has not been previously described. We report such a case that occurred at our institution in a 23-year-old man who underwent flap reconstruction for a cerebrospinal fluid leak. We determined that occlusion of the sphenoid sinus outflow might have played a role in this complication. The patient was treated via a combined surgical and medical approach that entailed a bur-hole craniotomy and endoscopic debridement followed by administration of an intravenous antibiotic. The patient recovered without long-term deficit. When closing a defect of the posterior ethmoid and sphenoid skull base, especially with a pedicled graft, care must be taken to reduce the potential for retention of secretions and blood because this may lead to an intracranial complication.