Budd–Chiari syndrome (BCS) is an uncommon disorder characterized by obstruction of hepatic venous outflow. The primary BCS is a rare disease with an incidence about 0.2 per million inhabitants per year. We present a 3-year-old boy with intrahepatic inferior vena cava clot. Because of decreased levels of protein C (38.7 %), F II (69.1 %), and activated protein C resistance (1.43), a mutational gene analysis was performed. The patient was found to be homozygous for the FV G1691A mutation. Conclusion: The primary BCS is a rare disease especially in childhood. Activated protein C resistance caused by the factor V Leiden mutation may be responsible for primary BCS. Prompt recognition of underlying prothrombotic disease and early initiation of their specific therapy might translate into rapid improvement of liver disease.