Objective <p>This study aimed to compare the efficacy of vacuum-assisted dedusting lithotripsy (VADL), employing a flexible vacuum-assisted ureteral access sheath (FV-UAS), with traditional flexible ureteroscopic lithotripsy (fURL) for upper urinary tract stones in patients with positive urine cultures.</p> Methods <p>A retrospective analysis was conducted on 421 patients treated with fURL between January 2022 and August 2024. Patients were divided into a traditional fURL group and a VADL group. Propensity score matching adjusted for baseline differences, with a 1:1 ratio applied to compare stone-free rates, operative durations, postoperative hospital stay durations, and postoperative infectious complications.</p> Results <p>Among 114 well-matched patients in each group, no mortalities occurred. The VADL group demonstrated significantly lower incidences of postoperative systemic inflammatory response syndrome (SIRS) (7.0% vs. 15.8%, <i>p</i> = 0.037) and shorter hospital stays (2.0 [1.0, 2.0] vs. 1.0 [1.0, 2.0], <i>p</i> = 0.014). The stone-free rate was significantly higher in the VADL group (87.7% vs. 72.8%, <i>p</i> = 0.005). However, no significant differences were observed in postoperative fever incidence or operative duration (7.0% vs. 9.6%, <i>p</i> = 0.472; 55.5 [40.0, 75.0] vs. 60.0 [45.0, 75.0], <i>p</i> = 0.104).</p> Conclusions <p>VADL significantly reduces postoperative infectious complications and enhances stone-free rates in patients with upper urinary tract stones and positive preoperative urine cultures undergoing ureteroscopic lithotripsy.</p>