A 73-year-old male, who had undergone hormonal therapy due to stage D2 prostate cancer, complained of fever up and appetite loss. Abdominal computed tomography showed emphysematous pyelonephritis and right ureteral stone. At first, we could not perform any surgical treatment due to disseminated intravascular coagulation and septic shock. After endotoxin absorption therapy, we performed transurethral retrograde drainage, and successfully treated the emphysematous pyelonephritis. Endotoxin absorption therapy should be performed before surgical treatment in cases of emphysematous pyelonephritis with severe general condition.