A 64-year-old woman who had a fever and low back pain was referred to our institution. Abdominal computed tomography revealed a low density area around the aorta and inferior mesenteric artery and liver abscess. Under the diagnosis of mycotic abdominal aneurysm, intravenous administration of antibiotics was started and her symptoms improved. On the 12th day after admission, the patient developed hematemesis and an emergency CT scan revealed enlargement of the low density area around the aorta and dilatation of the inferior mesenteric artery diameter to 16mm. Urgent operation was performed under the diagnosis of impending rupture of the mycotic aneurysm. Necrotic tissue and hematoma was recognized outside the aorta, and this mass firmly adhered to the duodenum. Communication between the abdominal aorta and the duodenum through the inferior mesenteric artery was confirmed. The infected aneurysmal area of the aorta was almost completely resected by closing the infra-renal aorta and terminal aorta above the bifurcation and a left axillo-femoral bypass was established. The culture of the necrotic tissue revealed Klebsiella pneumoniae. Antimicrobial therapy was continued and the patient was discharged from the hospital on postoperative day 46. Because the mortality rate of mycotic aneurysm penetrating to the duodenum is high, early diagnosis and treatment is important. We present a successfully treated case of mycotic aneurysm in which the formative course was observed from an early stage of infection. We observed the process of mycotic aneurysm formation and aorto-duodenal fistula generation despite antibiotic therapy. Close observation of periaortic inflammation and early surgical intervention is necessary in such patients.