A 43-year-old asymptomatic patient was diagnosed with an azygos vein aneurysm on contrast-enhanced computed tomography; at the 5-year follow-up, contrast-enhanced computed tomography revealed development of an azygos vein aneurysm. However, preoperative contrast-enhanced computed tomography at our hospital showed thrombus development along with shrinkage of the azygos vein aneurysm. To prevent thrombus dissemination, we decided to perform surgery. The aneurysm was excised via video-assisted thoracoscopic surgery, and the patient recovered uneventfully. Thoracoscopic surgery is effective in managing azygos vein aneurysms and preventing embolisms in thrombotic aneurysms. This procedure was chosen to avoid excessive compression of aneurysms and to prevent pulmonary embolism. This report presents a case of surgical management of an idiopathic azygos vein aneurysm with thrombosis.Clinical registration number 2020-S-20.