Abstract Background There is paucity of data on bacillus Calmette-Guérin (BCG) perfusion in patients with non–muscle-invasive urothelial carcinoma (NMIUC) of the upper urinary tract (UUT). Objective To assess the long-term results of BCG perfusion in patients with UUT NMIUC in terms of efficacy and tolerability. Design, setting, and participants Retrospective analysis of 55 consecutive patients (64 renal units RUs) with UUT NMIUC prospectively followed according to a standardised protocol for a median of 42 mo (range: 2–237 mo). Our series includes negatively selected patients, most of whom were not eligible for radical surgery, with additional invasive urothelial carcinoma of the urinary tract in roughly one-third of the cases. Intervention Antegrade BCG perfusion of the UUT was performed either with curative intent for carcinoma in situ (Tis; 42 RUs) or with adjuvant intent after ablation of Ta/T1 tumours (22 RUs). Measurements Primary outcome measures were recurrence-free, progression-free, and nephroureterectomy-free survival. The secondary outcome measure was treatment tolerability. Results and limitations Recurrence occurred in 30 of 64 RUs (47%), 17 of 42 (40%) with Tis and 13 of 22 (59%) with Ta/T1 tumours. Progression occurred in 11 of 64 RUs (17%), 2 of 42 (5%) with Tis and 9 of 22 (41%) with Ta/T1 tumours. Nephroureterectomy was eventually performed in 7 of 64 RUs (11%), 2 of 42 (5%) with Tis and 5 of 22 (23%) with Ta/T1 tumours. Patients treated with curative intent for Tis tended to have better recurrence-free survival ( p = 0.42) and significantly better progression-free survival ( p < 0.01) and nephroureterectomy-free survival ( p = 0.05) compared with those treated with adjuvant intent after ablation of Ta/T1 tumours. Adverse events, mostly minor, occurred in a total of 11 patients (20%), with one case of fatal Escherichia coli septicaemia. Conclusions In our patients with UUT NMIUC, antegrade BCG perfusion resulted in a high kidney-preservation rate. Patients treated with curative intent for Tis apparently benefited in terms of local disease control more than those treated with adjuvant intent after ablation of Ta/T1 tumours. Treatment tolerability was good.