Introduction: A retrospective analysis was conducted to identify factors associated with disease progression and intravesical recurrence (IVR) in a multi-centre cohort of patients with upper urinary tract urothelial carcinoma (UTUC) treated surgically between 2015 and 2021. Materials and Methods: Progression-free survival (PFS) and IVR-free survival were evaluated using a Kaplan–Meier survival curve and a Log-Rank test. Prognostic factors for progression and IVR were analysed using Cox logistic regression analysis. Results: A total of 170 patients were analysed. Up to 32.9% developed progression within 65.64 ± 3.44 months. Multivariate analysis showed that pT (HR 2.9, 95%CI 1.54–5.48, p = 0.01), margin status (HR 2.89, 95%CI 2.88–57.68, p = 0.01), and lymphovascular involvement (HR 7.97, 95% CI 1.43–44.42, p = 0.02) were independent risk factors for PFS. Up to 25.9% of patients presented with IVR at a mean time of 68.33 ± 3.59 months. A previous diagnosis of bladder cancer (BC) (HR 3.73, 95% CI 1.24–11.22, p = 0.02) and the non-invasive appearance of the tumour on computed tomography were significant risk factors for IVR (HR 0.23, 95% CI 0.05–0.95, p = 0.03). Conclusions: pT stage, margin involvement, and lymphovascular involvement were independent risk factors for UTUC progression. The main risk factor for presenting with IVR after UTUC was a previous diagnosis of BC.