Squamous cell carcinoma of the upper tract (SCC-UT) is a rare neoplasm that disproportionately affects patients with longstanding nephrolithiasis. Diagnosis is challenging and typically comes at late stages; as such, the prognosis is poor. The absence of a reliable diagnostic predictor for SCC highlights the need to keep the diagnosis in mind for at-risk patient populations. In this study, we describe a small case series of rapidly progressive SCC-UT incidentally discovered during percutaneous nephrolithotomy.