Fungal urinary tract infections are commonly encountered in the hospitalized neonate. Although these infections most commonly take the form of cystitis, the infection may be complicated by the formation of fungal bezoars, with subsequent urinary tract obstruction. In certain cases, endosurgical debulking or extraction of the fungal bezoar may be necessary. This is particularly challenging in neonates due to their often-compromised physiologic state and small size. We report a case of a premature infant with bilateral obstructing renal fungal bezoars in whom a percutaneous catheter-based thrombectomy system was used successfully to debulk the fungal burden.