Background <p>Reports on the incidence of urinary tract infections following flexible ureteroscopy in Palestine are scarce. This study aimed to assess the incidence of urinary tract infections after flexible ureteroscopy and to identify the risk factors that predict their occurrence among patients treated with this procedure in Palestinian clinical practice.</p> Methods <p>This was a prospective cohort study that aimed to assess the incidence rate of postoperative urinary tract infections among patients who underwent flexible ureteroscopy in Palestinian clinical practice. The study was conducted between October 2023 and January 2025 in four different hospitals in the West Bank of Palestine.</p> Results <p>A total of 253 patients were included in this study. Of the patients, 31 (12.3%) had urinary tract infections. <i>Enterococcus faecalis</i> was the most common causative agent. Multiple linear regression showed that the occurrence of post-flexible ureteroscopy urinary tract infections was significantly predicted by the postoperative red blood cell count (<i>p</i>-value = 0.033). Multivariate logistic regression demonstrated that patients with a documented urinary tract infection within the preceding 90 days had significantly greater odds of developing a post–flexible ureteroscopy urinary tract infection (OR = 3.34; 95% CI: 1.35–19.82). Furthermore, the absence of preoperative prophylactic antibiotic administration was independently associated with increased risk (OR = 4.66; 95% CI: 1.29–16.81) for a post–flexible ureteroscopy urinary tract infection.</p> Conclusion <p>The incidence rate of post-flexible ureteroscopy urinary tract infections in Palestinian clinical practice was within the range reported globally. The findings of this study emphasize the need for tailored, preventive measures, including enhanced preoperative risk assessment, optimized antibiotic management, and rigorous postoperative surveillance.</p>