We report a 56-year-old woman suffering from an embolic brain infarction in her right frontal lobe. Carotid ultrasonogram showed a mass-shaped thrombus with little atherosclerotic change of underlying intima-media in the right common carotid artery. The thrombus was reduced with treatment and changed to mobile slender thrombus on admission. No other embolic sources were detected even using transesophageal echocardiography. Her blood test indicated existence of antiphospholipid antibody syndrome (APS) complicated with mixed connective tissue disease as an etiology of this uncommon carotid thrombus. The thrombus disappeared completely after two-week intensive antithrombotic therapy. This is a valuable report that arterial thrombi accompanied by APS could be detected by carotid ultrasound and observed until thrombus was disappeared. When we manage APS patients, it is important to rule out thrombus formation in the carotid artery using ultrasonography from the point of stroke prevention.