BACKGROUND We describe a case of renal pelvi-ureteric fungus ball managed with placement of two nephrostomy tubes and amphotericin B irrigation through a nephrostomy tube with the other to free drain. METHODS A 46-year-old man with uncontrolled Type 2 diabetes mellitus was referred to the urology clinic for workup of recurrent urinary tract infection. Urine culture grew Candida albicans. The patient was started on oral fluconazole therapy. Cystoscopy and cystogram revealed a grade 3 left vesicoureteral reflux and right retrograde pyelogram revealed a filling defect in the right renal pelvis extending into the proximal ureter with severe hydroureteronephrosis. Two nephrostomy tubes were placed (mid-pole and lower pole) to ensure that the system was not obstructed. Amphotericin B (50 mg/1000 ml normal saline) irrigation was then instilled through the mid-pole nephrostomy tube at a rate of 30 ml/h with the lower pole nephrostomy tube to free drain. An antegrade nephrostogram was performed after 5 days of amphotericin B instillation, showing complete resolution of the fungus ball. The patient is awaiting definitive minimally invasive management of the distal ureteral narrowing. CONCLUSIONS Renal and pelvi-ureteric fungus ball is a challenging clinical entity. It must be addressed promptly and efficiently to be successful. We describe a minimally invasive approach that was tolerated well and resulted in complete clearance of the fungus ball in a relatively short time frame.