Upper urinary tract obstruction caused by fungal balls is a rare urinary system disease. We admitted an elderly man with symptoms of urinary tract infection and diabetes mellitus. When the patient was transported into the hospital, a CT scan revealed right renal pelvis dilatation and gas buildup, routine urinalysis showing full field of view of white blood cells and middle urinary bacteria and fungi cultures came back negative, leading to the incorrect diagnosis of emphysematous pyelonephritis with Aerogenes infection. When the diagnosis is confirmed, surgery and antifungal therapy are used to deal with both the obstruction and the fungal ball.