Keratinizing desquamative squamous metaplasia (KDSM), also known as leukoplakia or cholesteatoma, of the genitourinary tract is a rare condition that is difficult to differentiate from a malignant process without surgical intervention. We present a case of KDSM of the upper urinary tract that was managed via percutaneous endoscopic approach. Although KDSM is a benign lesion, there are rare reports of it occurring concurrently with squamous-cell carcinoma; however, no direct causal relationship has been identified. This case demonstrates the ease with which KDSM can be removed by peeling it away from the underlying parenchyma; however, surgical intervention may not be necessary in the asymptomatic patient after evaluation has ruled out malignancy. Regardless of how KDSM is managed, follow-up is important because these lesions are known to recur.