Urothelial tumors in patients with anatomical abnormalities may pose significant challenges. Management follows the same principles which are employed in normal anatomy, however, thorough diagnostic investigation is warranted in order to delineate key anatomical landmarks. Meticulous pre-operative investigation should utilize every imaging modality which can assist the surgeons. We present a case of transitional cell carcinoma (TCC) in a crossed-fused kidney treated with nephro-ureterectomy. Only a handful of cases of TCC in CFRE have been reported. The case demonstrates the critical role of pre-operative anatomical studies and intra-operative identification of unique anatomy, which facilitate treatment and avoid complications.