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A 60-year-old man with a history of Raynaud’s phenomenon presented with bilateral intermittent claudication and an ulcer on his right toe. The ankle–brachial index of the right and left legs was 0.77 and 0.75, respectively. Laboratory data showed prolongation of the activated partial thromboplastin time and a positive result on the lupus anticoagulant test. Computed tomography angiography revealed isolated infrarenal aortic stenosis with irregular surface and noncalcified plaques. Intravascular ultrasonography examination demonstrated a noncalcified, irregular, and mobile plaque, suggestive of abdominal aortic thrombosis. In addition to anticoagulant and dual antiplatelet therapy, endovascular treatment was performed. A total of three 40-mm-long balloon-expandable stents were successfully implanted on a 15-mm balloon. The final angiography showed good results except for minimal plaque shifting in the terminal aorta. Three months later, the ulcer resolved and a final diagnosis of primary antiphospholipid syndrome (APS) was made. Clinicians should recognize that APS can affect the abdominal aorta, leading to aortic thrombosis. Endovascular treatment may be the one good treatment option for this rare condition.