Aortic dissection is a life-threatening illness requiring early diagnosis and treatment. Uncommon early presentations mimicking various illnesses can delay diagnosis. This case study describes a 44-year-old woman with type B aortic dissection initially presenting as acute pyelonephritis (APN). Early clinical manifestations were sudden onset of left flank pain, fever, hematuria and pyuria, and following admission, severe abdominal pain, nausea, vomiting, reduced urine output and renal function deterioration. Abdominal computed tomography showed type B aortic dissection complicated with a small bowel infarct, ischemic ascending colon and left renal infarct. Emergency surgical interventions of small bowel resection, ileoduodenostomy and cholecystectomy were performed; a second laparotomy was subsequently performed for anastomosis leakage. The patient died due to septic shock with multiorgan failure. Aortic dissection initially mimicking APN is rare. Accurate early diagnosis of aortic dissection with indeterminate presentation is crucial. Early surgical intervention for visceral organ ischemia is important to preventing morbidity and mortality.