Background: Shock wave lithotripsy (SWL) and flexible ureterorenoscopy (FURS) have been used to treat renal stones. Objective: This study aimed to compare the results of FURS and SWL in managing post- percutaneous nephrolithotomy residual stone particles. Subjects and Methods: This prospective randomized controlled study included 48 patients with renal residual stones. It was conducted at Urological Department, Zagazig University Hospitals to compare the outcomes of SWL and FURS for the treatment of residual stone fragments from ≥ 4 mm to ≤ 20 mm following percutaneous nephrolithotomy (PNL). Results: The success rate, operating time, residual stones, and complications in the two groups were all significantly different. One month following surgery, the SFR was higher in the FURS group (91.7%) than in the SWL group (66.7%) (p < 0.02). Less time was spent operating on patients in the SWL group (37.6 ± 7.63) than FURS group (57.50 ± 8.84). Complication rate was 16.6% in the SWL group and 12.5% in the FURS group. Conclusion: Treatment of 0.4–20 mm residual stone fragments following PNL using FURS, SWL, and other techniques was found to be safe and successful in all cases. Compared to SWL, the SFR of FURS was greater, and the retreatment rate was lower. The operating duration in the FURS group was the longest.