Inherited antithrombin deficiency generally causes a predisposition toward vascular thrombus above the age of 15 years. A 1-year-old boy developed renal hypertension caused by renal artery obstruction due to thrombus formation. This thrombus formation was attributed to antithrombin deficiency caused by a novel SERPINCI gene mutation (AT III Akita, M352R). This suggests that antithrombin deficiency can cause renal artery obstruction, inducing renal hypertension through vascular thrombosis even in children.