A 21-year-old man presented with aspergilloma in the prepontine cistern that developed after treatment for cerebellar hematoma following rupture of an arteriovenous malformation. He became bedridden with neurological signs of tetraparesis, disturbed ocular movement, and bulbar palsy, despite alert consciousness. Repeat magnetic resonance imaging 1 year later revealed a space-occupying lesion in the prepontine cistern along the clivus. This multilobular enhanced mass lesion gradually enlarged towards the brainstem over the following 4 years, resulting in loss of spontaneous breathing and dependence on a mechanical respirator. Surgical treatment via a lateral suboccipital approach was selected to reduce the size of the mass lesion and confirm the diagnosis. Histological examination revealed the presence of Aspergillus fumigatus. Treatment with amphotericin B (1 mg/kg/day) and fluconazole (100 mg/kg/day) injected into the peripheral veins was initiated, but was stopped due to the appearance of renal dysfunction. An Ommaya tube was then inserted into the prepontine cistern via a transsylvian approach to provide high concentrations of amphotericin B around the granulomatous lesion. He gradually improved, corresponding to the decreased size of the aspergilloma just after surgery. Surgical reduction of granuloma combined with local administration of antifungal agent is a good treatment option in patients with aspergilloma refractory to systemic administration.