A 44-year-old man presented with a very rare case of skull base osteomyelitis manifesting as persistent diplopia. He initially had the symptom with fever after dental extraction. Biopsy from the cervix and upper pharynx performed in a previous hospital had showed negative findings by histological and bacterial examinations. Magnetic resonance (MR) imaging disclosed enhanced lesions in the right cavernous sinus, clivus, and right cervical regions. Computed tomography revealed osteolysis, and fluorodeoxyglucose positron emission tomography (FDG-PET) showed areas of increased uptake. Bacteriological examination of the isolated clival lesion disclosed Actinomyces israelii, and he was treated with intravenous penicillin, 18 million units a day for 6 weeks. MR imaging revealed reduction of intensity in the enhanced areas, and FDG-PET showed disappearance of the increased uptake. After 6 months of oral antibiotics administration, MR imaging disclosed disappearance of the enhanced lesions, and the patient had no sign of neurological deficits. Skull base osteomyelitis resembles neoplasm or inflammatory disease of this region in neurological and radiographic findings. The biopsy specimen should be ideally obtained from an isolated region, and prepared to identify a wide range of organisms and to differentiate other diseases. The serum level of C-reactive protein and FDG-PET are useful to follow up the efficacy of antibiotic therapy.