Invasive non-typhoidal Salmonella (NTS) infections are rare in developed countries but their incidence is increasing. One of the most severe complications of extraintestinal NTS infection is mycotic aneurysm. Its natural course is usually fatal and its treatment demands complex interdisciplinary management. We present a case of severe NTS sepsis complicated by mycotic aneurysm of the abdominal aorta and left internal iliac artery and obstructive pyelonephritis. Obstruction of the left ureter was caused by pressure from the left internal iliac artery aneurysm and surrounding edema. The patient presented with clinical symptoms of sepsis and pyelonephritis. Despite abdominal ultrasound and native computed tomography, the mycotic aneurysm eluded initial examination. It remained undiagnosed until the patient presented with recurrent symptoms after stopping 17 days of antimicrobial treatment and was finally revealed by magnetic resonance imaging and contrast computed tomography. The patient was successfully treated by ligation of the left internal iliac artery, partial extirpation of the aneurysm and prolonged parenteral antimicrobial treatment. This case raises concerns that mycotic aneurysm might be present in cases of obstructive pyelonephritis caused by NTS and its early recognition is vital for appropriate management.