Microscopic polyangiitis (MPA) is a type of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis linked to myeloperoxidase (MPO), usually accompanied by pulmonary and renal lesions. MPA sometimes causes central nervous system (CNS) involvement such as cerebral infarction. Herein, we report a case of a 72-year-old man with a headache. He had an unknown cause of the elevated inflammatory response. Magnetic resonance imaging (MRI) showed multiple cerebral infarctions in the small vessel region in the right basal ganglia with multiple cerebral microbleeds (cMBs). After admission, his left hemiparesis and consciousness disturbance gradually deteriorated. A follow-up MRI on day 18 showed increased multiple cerebral infarctions in small vessel regions with increased cMBs. Additional blood tests revealed positive MPO-ANCA. Although there were no findings suggestive of active renal or pulmonary involvement or peripheral neuropathy, we diagnosed him as having MPA-associated CNS-restricted vasculitis. CNS involvement of MPA is relatively rare but is associated with a high small vessel disease (SVD) burden. In addition to the unknown cause of inflammatory response, the multiple cMBs increase and a short-term recurrence of cerebral infarctions in the bilateral thalamus and basal ganglia was the clue for the diagnosis of CNS-restricted vasculitis. It is difficult to diagnose MPA vasculitis when lesions are restricted to the CNS. In the absence of lesions other than SVD, MPA-associated CNS vasculitis should be suspected in patients with progressive SVD burden and elevated inflammatory response.