Previous studies have reached diverse conclusions about the influence of tumor size on the oncologic outcomes in patients with upper tract urothelial carcinoma (UTUC). In this study, we retrospectively analyzed the records of 687 patients and evaluated how tumor size affected the prognosis of patients with UTUC after surgery. Clinicopathologic characteristics and oncological outcomes were compared according to tumor size (≤3 cm versus >3 cm). During a median follow-up period of 65 months (range 3-144 months), 225 patients (32.8%) died from UTUC and 228 patients (33.2%) experienced intravesical recurrence (IVR). Patients with a larger tumor size tended to have a significantly higher percentage of being male (p = 0.011), tobacco consumption (p = 0.036), lack of preoperative ureteroscopy history (p = 0.003), renal pelvic location (p < 0.001), tumor necrosis (p = 0.003), advanced tumor stage (p < 0.001), higher tumor grade (p = 0.003), and lymph node metastasis (p = 0.018). Univariate analysis revealed that a tumor size >3 cm was significantly associated with worse cancer-specific survival (p = 0.002) and IVR (p = 0.011). However, the influence was not statistically significant after controlling for other factors in the multivariate analysis (hazard ratio [HR] 1.124, p = 0.414 and HR 1.196, p = 0.219). In conclusion, UTUC patients with a larger tumor present aggressive biological characteristics and tend to have a worse prognosis.