Background/Objectives: We assessed factors affecting the oncological outcomes in upper tract urothelial carcinoma patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD) in Taiwan, using a large domestic upper tract urothelial carcinoma collaboration database. Methods: From July 1988 to December 2019, 15 hospitals joined the Taiwan Upper Tract Urothelial Carcinoma Collaboration Group. A total of 690 patients were included, and demographic, clinical, and pathological data were compared. Factors related to overall survival, cancer-specific survival, disease-free survival, and bladder recurrence-free survival were analyzed. Results: Out of the 690 patients, 605 had CKD and 85 had ESRD. In multivariate analysis, overall survival was associated with CKD stage (p = 0.024), age > 70 years (p = 0.002), and pathological stage III/IV (p = 0.014 and <0.001). Cancer-specific survival was associated with middle ureter tumors (p = 0.041), positive surgical margin (p = 0.005), and pathological stage III/IV (p = 0.010 and <0.001). Disease-free survival was associated with middle ureter tumors (p = 0.001), lower ureter tumors (p = 0.010), and pathological stage III/IV (p = 0.039 and <0.001). Female sex (p = 0.027), lower ureter tumors (p = 0.027), coronary artery disease (p = 0.047), and arrhythmias (p = 0.044) were associated with bladder recurrence-free survival. Conclusions: The oncological outcomes of UTUC patients with CKD and ESRD in Taiwan were affected by various factors. Tumor location and advanced pathological stage were related to OS, CSS, and DFS. Cardiac diseases were possibly related to BRFS.