Objective There is ongoing debate regarding whether patients with a positive urine culture (UC) need to wait for the culture to turn negative following antimicrobial treatment before undergoing percutaneous nephrolithotomy (PCNL). This study aimed to evaluate the necessity of achieving a negative UC before PCNL and its association with postoperative systemic inflammatory response syndrome (SIRS) and sepsis. Methods This prospective study included 147 patients with positive UCs who underwent PCNL at The First Affiliated Hospital of Guangzhou Medical University from March 2021 to April 2024. Patients were treated with sensitive antibiotics for 5-7 days based on the susceptibility results of their initial UC. Follow-up UCs were performed on day 3 after starting antibiotics and immediately before surgery. The relationship between UC results and postoperative infectious complications, including SIRS and sepsis, was analyzed. Multivariable analysis was conducted to identify independent risk factors.occurrence of postoperative infectious complications, including SIRS and sepsis, was analyzed. Multivariable analysis was used to identify independent risk factors. Results Among the 147 patients, 133 (90<middle dot>5%) had a negative urine culture on day 3 of treatment, while 14 remained positive. Preoperatively, 136 patients (92<middle dot>5%) had negative UCs. Univariate analysis showed no significant differences in the incidence of postoperative systemic inflammatory response syndrome (SIRS) and sepsis between the UC-negative and UC-positive groups on day 3 and preoperatively (p > 0<middle dot>05). Multivariable analysis identified stone burden (OR 1<middle dot>01, 95% CI 1<middle dot>01-1<middle dot>01, p = 0<middle dot>009), multiple access tracts (OR 2<middle dot>64, 95% CI 1<middle dot>08 - 6<middle dot>45, p = 0<middle dot>034), and positive stone cultures (OR 5<middle dot>03, 95% CI 1<middle dot>84 - 13<middle dot>74, p = 0<middle dot>002) as independent risk factors for postoperative SIRS. Bacterial variations were observed in follow-up UCs from 8 patients, but these did not impact postoperative complications. Conclusion Achieving a negative UC before PCNL is not a necessary condition. Patients with positive UCs can safely undergo surgery after 5 days or more of sensitive antibiotic treatment without the need for a negative UC result. Positive stone cultures are valuable predictors of postoperative SIRS, supporting the routine collection of stone culture specimens.