Catheter-related right atrial thrombus (RAT) is an uncommon life-threatening complication. Few cases of endovascular cooling catheter–related complications have been reported. We report the first case of endovascular cooling catheter–related RAT. A 17-year-old adolescent boy was treated with therapeutic hypothermia using an endovascular cooling catheter following ventricular fibrillation cardiac arrest. He became alert, but RAT was found 3 days after the placement of the cooling catheter. Anticoagulation with enoxaparin for 2 weeks completely resolved the RAT, and he was consequently treated with radiofrequency ablation and received an implanted cardiac defibrillator. This case report highlights the occurrence of endovascular cooling catheter–related RAT early after the placement of a catheter. Physicians should monitor whether RAT occurs during and following therapeutic hypothermia with a cooling catheter.