Purpose: To compare the long-term outcomes of the most widely used third-generation stent grafts, the Endurant and Excluder stent grafts, in Japanese patients using a multicenter registry. Materials and Methods: A retrospective analysis of endovascular aneurysm repairs for abdominal aortic and iliac artery aneurysms using either the Endurant or the Excluder stent grafts from January 2012 to July 2019 at 10 Japanese hospitals was performed. Results: A total of 332 and 378 repairs using the Endurant and Excluder stent grafts, respectively, were analyzed. Although the patients’ characteristics were generally similar in the two groups, the Endurant group exhibited significantly shorter (Endurant: 31.5±18.6 mm, Excluder: 37.4±21.0 mm; p<0.001), larger (Endurant: 22.4±4.2 mm, Excluder: 21.7±3.8 mm; p=0.029), and more reversed tapered (Endurant: 12.1%, Excluder: 5.8%; p=0.003) proximal necks. The incidence of instructions for use (IFU) violations was similar between the two groups (Endurant: 59.0%, Excluder: 54.5%; p=0.223). However, the Endurant group had significantly more proximal neck-related IFU violations (54.1% and 46.3%, respectively; p=0.039), more access-related IFU violations (8.1% and 4.0%, respectively; p=0.019), and fewer bilateral hypogastric artery embolizations (5.1% and 9.3%, respectively; p=0.035) compared with the Excluder group. The incidence of intraoperative (Endurant: 3.6%, Excluder: 3.7%; p=0.950) and perioperative complications (Endurant: 3.6%, Excluder: 3.4%, p=0.899) was equivalent in the two groups. However, there was a significantly higher incidence of postoperative type II endoleaks in the Excluder group (Endurant: 28%, Excluder: 46.0%, p<0.001). Aneurysm sac regression was more frequent in the Endurant group (Endurant: 40.7%, Excluder: 31.7%, p=0.013). The Endurant group also had significantly higher rates of sac increase (Endurant: 13.0%, Excluder: 7.7%, p=0.020). Kaplan-Meier curve and log-rank analyses revealed no statistical differences in late complications (p=0.868) and overall survival (p=0.926). Conclusions: There were no statistically significant differences between the Endurant and the Excluder stent grafts in terms of intraoperative, perioperative, and late complication rates; however, the anatomical characteristics of the patients were significantly different.