Introduction: Duplication of the inferior vena cava (IVC) is a congenital venous malformation that occurs in 0.2%–3% of the population as a result of persistent left and right supracardinal veins. The IVC duplication is prone to deep vein thrombosis due to endothelial dysfunction and associated venous stasis. This is a rare case of recurrent venous thrombosis due to IVC duplication and decreased protein C activity. Case: A 57-year-old male presented with swelling of the left lower limb that gradually developed over a one-week period preceding his visit. He reported a history of superior mesenteric vein thrombosis, approximately three years ago, for which he received anticoagulation therapy for three months. Thoracoabdominal contrast-enhanced computed tomography (CT) revealed thrombi in the locations of the bilateral main pulmonary arteries, IVC duplication, left common iliac vein, left IVC, and left renal vein. Blood work confirmed protein C activity of 21% (baseline 64%–146%), that could have contributed to the recurrent IVC thrombosis and formation of pulmonary artery thrombus. Subsequently, the patient was hospitalized and started on anticoagulation therapy. The swelling in the left lower extremity gradually improved, and the patient was instructed to continue anticoagulation therapy permanently. Conclusion: When investigating venous thrombosis of unknown or recurrent origin, it is necessary to include venous malformations and abnormal activity of blood coagulation factors in differential diagnosis.