We report a 56-year-old man with microscopic polyangiitis (MPA) who developed acute exacerbation of a chronic subdural hematoma (SDH). Laboratory data demonstrated elevation of myeloperoxidase antineutrophil cytoplasmic antibody (MPOANCA) and rapidly progressing renal dysfunction. Renal biopsy showed crescentic glomerulonephritis (GN) with membranous nephropathy (MN). He was treated with corticosteroids, antithrombotic agents, and an immunosuppressant. One month after initiation of treatment, he had a mild headache. One month later, he developed acute SDH. Although he recovered completely after the operation, he finally died of bacterial infection. On autopsy, a scar of vasculitis was confirmed in the leptomeninges as well as in the kidney and lung. Although SDH is a rare complication in MPA, nephrologists must pay more attention to the initial symptoms before a hematoma attack such as headache, especially in patients using antithrombotic agents.