A 66-year-old man was admitted to our hospital because of a low-grade fever and arthralgia. The symptoms started on the third day after influenza vaccine administration and persisted for two months. Serum creatinine was 1.0 mg/dL; C-reactive protein, 16.1 mg/dL; and myeloperoxidase antineutrophil cytoplasmic antibodies (MPO-ANCA), 4,170 IU/mL. A kidney biopsy showed crescentic glomerulonephritis with fibrinoid necrosis of small arteries. Microscopic polyangiitis was diagnosed. After five months of steroid pulse therapy and rituximab administration, the patient entered remission. There have been very few reports of this condition after influenza vaccine administration.