Spontaneous cerebrospinal fluid (CSF) leakage at the clivus is rare. In previous reports, reconstructive materials used to treat such leakage were typically autografts. Considering the pathology, rigid reconstruction is preferred. We here describe a case of spontaneous CSF leakage at the clivus with multiple bony defects. In this case, in addition to using artificial material instead of autografts, such as fat or fascia, that require additional extranasal invasive harvesting site, a rigid material layer of septal cartilage and bone was also used, enabling more stable multilayer reconstruction. One month postoperatively, computed tomography revealed that the bony defect at the clivus had been well reconstructed. All nasal structures were preserved, and the nasoseptal flap was well engrafted. At eight months post-surgery, the patient remained in good condition. This method allows minimally invasive repair of the leaking clivus, according to the underlying pathophysiology.