We report a case of primary central nervous system vasculitis (PCNSV) diagnosed by second brain biopsy. A 53-year-old man initially presented with left lateral gaze diplopia. Brain MRI revealed multiple enhanced lesions in the bilateral frontal lobe, bilateral basal ganglia, left cerebellum and brainstem. An initial brain biopsy of the right frontal lobe suggested immune-related encephalitis with angiocentric accumulation of chronic inflammatory cells, while malignant lymphoma could not be completely ruled out. The patient deteriorated despite being treated with repeated methylprednisolone pulse therapy, cyclophosphamide, and plasmapheresis. A second brain biopsy of the right temporal lobe was then performed. The biopsied specimens showed vascular wall disruption and fibrinoid necrosis with perivascular inflammatory infiltrates, mainly composed of CD8-positive T cells, and PCNSV was diagnosed. He was treated with high dose corticosteroids, in combination with methotrexate (8 mg/week), which reduced the brain lesions. As brain biopsy is an essential investigation for the histological diagnosis of PCNSV; subsequent biopsies may be required when a histopathological diagnosis has not been obtained by the first biopsy, and further aggressive therapy is being considered.