This study assessed the impact of urinary tract anomalies or a history of upper urinary tract surgery (UTAS) on the minimally invasive endoscopic combined intrarenal surgery (mini-ECIRS) outcomes. Data from 1432 patients undergoing ECIRS for urolithiasis at three Japanese tertiary institutions between 2015 and 2021 were analyzed, with patients categorized into those with normal urinary tracts (non-UTAS) and those with UTAS (UTAS). We retrospectively examined the association between the UTAS and perioperative outcomes in mini-ECIRS. Of the 1096 cases in the final analysis, 1035 and 61 were identified as non-UTAS and UTAS, respectively. Stone-free rate (residual fragments > 2 mm, 62.8% vs. 62.7%), operation time (110.5 vs. 115.0 minutes), and hospital stay duration (5.6 vs. 5.7 days) showed no significant differences between non-UTAS and UTAS. The UTAS group demonstrated significantly higher rates of preoperative pyuria (86.2% vs. 71.1%), preoperative urinary tract infection (32.8% vs. 15.5%), preoperative stenting (52.5% vs. 31.0%), and preoperative nephrostomy (24.6% vs. 9.2%). However, the postoperative fever (26.3% vs. 25.0%) or septic shock (1.9% vs. 0%) were comparable between non-UTAS and UTAS. Stone burden and the number of calyces involved were significantly associated with a low stone-free rate (P < 0.001). Younger age, female sex, solitary stones, number of calyces involved, preoperative urinary tract infection, and absence of preoperative nephrostomy were identified as risk factors for perioperative complications. The UTAS was not associated with stone-free outcomes or perioperative complications. Mini-ECIRS demonstrated comparable stone-free outcomes and safety in patients with UTAS and those with normal urinary tracts.