To identify the risk factors for perioperative complications to prevent perioperative complications after complete ipsilateral upper urinary stone removal using flexible ureterorenoscopy. We retrospectively examined 111 patients who underwent flexible ureterorenoscopy for ipsilateral renal stones with a diameter ≥ 5mm at the same time as ureterorenoscopy for ureteric stones. The flexible ureterorenoscopy procedures were performed following the fragmentation technique. Patients who experienced (complication group) and did not experience (non-complication group) perioperative complications were compared. The complication group included 33 patients with Clavien-Dindo classification scores of I, II, III, or IV and/or those with a body temperature of > 37.5℃ during hospitalization. The overall stone volume, stone-free rate and procedure duration were 1.71mL, 96.4% and 77min, respectively. The rate of perioperative complications was 29.7% (grade 1, 2 and 3 was 23.4%, 5.4% and 0.9%, respectively). Severe complications (Clavien-Dindo grade 4) were not observed. Multivariable analysis revealed that ureteral stone volume and female patients were independent predictors of perioperative complications after flexible ureterorenoscopy (p = 0.015 and 0.017, respectively). This study showed that ureteral stone volume and female gender have the possibility to increase perioperative complications. These preliminary data help to select for patients who are at low risk of complications. Therefore, in these selected patients, complete ipsilateral upper urinary tract stone removal using flexible ureterorenoscopy may reduce the recurrence of urolithiasis without increasing perioperative complications.