A 52-year-old male, with diabetes mellitus and alcoholic liver disease, presented to the Emergency Room for right flank pain of 3 days' duration, associated with dysuria. Physical examination revealed right flank tenderness with fever and hypotension; laboratory findings showed acute kidney injury and large blood and leucocytes in the urine. A CT abdomen and pelvis showed hydronephrosis of the right collecting system of a horseshoe kidney with air and hyperdense debris in the renal pelvis. Patient was treated for multisensitive Proteus mirabilis emphysematous pyelonephritis, and a right nephrostomy tube was inserted. Symptoms recurred in 4 weeks, and repeated urine culture grew Candida albicans and CT scan showed same high density material within the right moiety of the horseshoe kidney. Patient underwent ureteroscopy, and a white fluffy material was aspirated from the right renal pelvis. Pathology of the aspirate confirmed the presence of fungal balls. Patient was given 2 weeks of oral fluconazole. Fungal pyelonephritis is unusual and difficult to treat. Candida species is responsible for the clear majority of the cases. A fungus ball should be managed with surgical and medical therapy. This patient had an endoscopic procedure to remove the fungus ball and received fluconazole. His symptoms resolved and urine culture was done before termination of the treatment was negative.