ABSTRACT Purpose To identify risk factors of infectious complications following mini‐endoscopic combined intrarenal surgery (ECIRS) in patients with renal or ureteral stones. Methods We retrospectively analyzed consecutive patients with renal or ureteral stones who underwent mini‐ECIRSs at three Japanese tertiary institutions between 2015 and 2021. Data were collected and evaluated regarding patient backgrounds, stone characteristics, and postoperative complications. Among the various complications, multivariable logistic regression analysis was performed using preoperative and intraoperative factors for postoperative fever (≥ 38°C) and septic shock to identify independent risk factors. Results The data of 1432 cases were collected. Finally, 1035 cases of single‐session mini‐ECIRS were included in the analysis. In infectious complications, postoperative fever and septic shock were observed in 273 and 21 patients (26.4% and 2.0%). A multivariable logistic regression model identified female ( p < 0.001), ureteral stones ( p < 0.001), preoperative pyuria ( p < 0.001), preoperative urinary tract infection ( p = 0.045), preoperative percutaneous nephrostomy ( p = 0.001), and operation time ( p = 0.017) as predictors of postoperative fever. For septic shock, female ( p < 0.001) was shown as a risk factor. Conclusions To the best of our knowledge, this multicenter cohort study is the largest study investigating infectious complications following mini‐ECIRS. Female was a common risk factor for both postoperative fever and septic shock, suggesting that surgeons should pay extra attention to vital signs during the procedure and postoperative infectious complications in mini‐ECIRSs for these patients.