A 63-year-old male patient with hematuria and flank pain was admitted. Radiological evaluation revealed S-shaped, left-to-right cross-renal ectopia with a renal mass localized in the upper pole of the right kidney. Three-dimensional computed tomography (3D-CT) showed that the orthotopic moiety had 1 artery and 2 veins, and the ectopic moiety had 1 artery and 1 vein. A nephron-sparing partial nephrectomy was performed. The pathological diagnosis was collecting duct carcinoma with sarcomatoid differentiation. Using 3D-CT, we were able to achieve the appropriate pre-operative surgical planning for this challenging case. To our knowledge, this is the first case report of collecting duct carcinoma with sarcomatoid differentiation in a cross-fused renal ectopic kidney.