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Abstract Background We herein present a case of venous thrombosis that developed more than 20 years after diagnosis of granulomatosis with polyangiitis (GPA), although many reports of GPA have described venous thrombosis within 1 year of diagnosis. Case presentation A 73-year-old man with GPA was admitted for lower extremity swelling and diagnosed with venous thrombosis and pulmonary embolism. On the second day, catheter-based thrombolysis was unsuccessful, and inferior vena cava filter insertion and anticoagulation were performed. On the third day, respiratory disturbance and loss of consciousness appeared and progressed. The patient died on the fifth day. The autopsy revealed a large thrombus in the inferior vena cava filter, and death of progressive venous thrombosis was suspected. Conclusions We experienced a case of venous thrombosis that developed 20 years after diagnosis of GPA, although GPA is frequently associated with venous thrombosis immediately after diagnosis. The thrombosis progressed rapidly and was resistant to treatment.