Background Thromboembolism associated with catheter ablation of atrial fibrillation has been considered to be derived from catheters, ablation sites, or a left atrial appendage. Paradoxical brain embolism due to iatrogenic shunt after catheter ablation has yet to be described. Methods We described a patient with atrial fibrillation who developed acute ischemic stroke while coughing 36 hours after successful catheter ablation. He had venous thrombosis due to heparin-induced thrombocytopenia and a right-to-left shunt, likely due to a trans-septal puncture during catheter ablation. Results The final diagnosis was paradoxical brain embolism associated with heparin-induced thrombocytopenia. Conclusions In addition to anticoagulation, we should pay attention to deep venous thrombosis including preventive intermittent compression for high-risk patients to reduce the risk of stroke after catheter ablation.