Invasive candidiasis is a serious pathogen of late-onset sepsis in very low birth weight infants. Kidney is the most common organ involved, and it causes morbidity and mortality, especially when fungal balls are formed. We report a 34-day-old female infant (born at 28 weeks' gestation, 1152 g) with systemic fungal infection complicated obstructive uropathy. On sonography, the fungal balls filled the entire pelvis without hydronephrosis. Percutaneous nephrostomy was not feasible. In addition to systemic antifungals, we successfully performed cystoscopy-assisted retrograde ureteral catheterization to decompress the pelvis, which also provided a route for local amphotericin B irrigation to achieve therapeutic concentration without nephrotoxicity.