Background: Mycotic aneurysms (MAs) are relatively rare but life-threatening. Some recent reports have described the use of endovascular therapy for their treatment; however, this still is a controversial treatment, and a definite target population has not been determined. Methods: We performed surgery on 34 patients with MAs from March 2005 to March 2019. Twenty patients who underwent open surgery (OS) first comprised the OS group, and 14 patients who underwent endovascular therapy first comprised the stent-graft (SG) group. We analyzed between-group differences, long-term outcomes, and risk factors for death retrospectively. Patients in the OS group had a higher initial white blood cell count than those in the SG group (p = 0.047). The SG group had more patients with a low albumin concentration (£2.0 mg/dL) than did the OS group (p = 0.026). Results: There were no significant differences in the operative mortality rates between the groups (p = 0.773). Additional procedures were required more often in the SG than the OS group (p = 0.0013). The overall survival rate as estimated by the Kaplan-Meier method was 88% at 1 month, 67% at 1 year, 57% at 3 years, and 45% at 10 years. In the univariable analysis, chronic obstructive pulmonary disease (COPD) was a risk factor for death (p = 0.003). Conclusions: Endovascular therapy for MAs produced reasonable outcomes when patient selection was based on the activity level, nutritional condition, and degree of inflammation. Endovascular therapy may become an option for patients with a low albumin concentration or COPD despite the fact that additional procedures may be needed.