We report a case of emphysematous pyelonephritis coexisting with emphysematous cystitis. A 57-year-old woman seen for abdominal pain, diarrhea, and high fever had been referred after computed tomography (CT) elsewhere had shown an air density mass in the left kidney and pelvis. Abdominal CT on admission showed emphysematous change in the left renal parenchyma and intramural bladder. Serum analysis results showed disseminated intravascular coagulation (DIC) and uncontrolled diabetes. Klebsiella pneumoniae was isolated in the blood. She was diagnosed with sepsis based on these findings due to concurrent emphysematous pyelonephritis and cystitis caused by K. pneumoniae. She was treated conservatively with meropenem, intravenous immunoglobulin, and gabexate mesilate and cured. Concurrent emphysematous cystitis and pyelonephritis is rare., with ours only the fourth case reported in Japan.