Herein, we present a neonatal case of coarctation of the aorta, with aortic arch thrombus confirmed by echocardiography. We performed thrombus removal and aortic arch repair emergently. This critical condition necessitates quick preoperative evaluation with echocardiography. Moreover, postoperative evaluation using computed tomography is reasonable to assess an aortic arch configuration, and exclude the remnant thrombus.