Abstract Background Primary squamous cell carcinoma (SCC) of the kidney is a rare entity which tends to be associated with nephrolithiasis, chronic irritation, and infection. Due to its rarity and the non-specific clinical signs and symptoms as well as radiological findings, it is often not suspected preoperatively. Patients with SCC of the renal pelvis typically present with advanced stage disease and have a poor outcome. Most of our current knowledge of SCC of the renal pelvis has been derived from case reports or limited case series, and there are no standard treatment guidelines. The clinical, radiological, and histopathological findings of this unusual neoplasm are described herein. Case presentation A 61-year-old female presented with left flank pain and sepsis. A computerized tomography (CT) scan showed renal calculi and hydronephrosis, and a mercapto-acetyl triglycine (MAG-3) scan showed a left-sided non-functioning kidney. She underwent a nephrectomy for an infected, non-functioning kidney. Histopathological examination revealed an invasive, moderately differentiated squamous cell carcinoma. Conclusion The significance of this case is highlighted by the unusual location of such a tumour, and while rare, it is an important consideration in the differential diagnoses of renal tumours. The present case report may assist patient management of this rare tumour by highlighting and documenting treatment and clinical outcome of our patient.