Venoarterial extracorporeal membrane oxygenation (VA-ECMO) is a critical treatment for patients with massive pulmonary embolism (PE) complicated by refractory cardiogenic shock. In this case, an inferior vena cava (IVC) filter and iliac vein thrombosis posed a risk of filter migration with conventional femoral venous access, necessitating an alternative drainage approach. We treated an 18-year-old male with hereditary thrombophilia due to a prothrombin gene (F2) mutation who presented with acute massive PE and cardiogenic shock. Following emergency pulmonary artery thrombectomy and IVC filter placement, VA-ECMO was initiated using right internal jugular vein cannulation for venous drainage and femoral artery cannulation for arterial return. Hemodynamic stability was rapidly achieved, allowing successful weaning and decannulation within 96 h. The patient was discharged on postoperative day 11 without neurological complications. This case demonstrates that jugular-to-IVC cannulation is a feasible and effective VA-ECMO drainage strategy for patients with existing IVC filters, avoiding mechanical complications associated with filter traversal.