Background: Despite technology incorporation to percutaneous nephrolithotomy (PCNL), residual stone fragments (RSFs) may still persist after PCNL and need to be addressed to avoid regrowth or ureteral obstruction. The objective of this study was to compare the outcomes of retrograde intrarenal surgery (RIRS) to extracorporeal shockwave lithotripsy (SWL) for treating patients with RSFs after a previous standard PCNL. Materials and Methods: Adult patients with RSF after a standard PCNL submitted to RIRS or SWL in our Institution from January 2017 to January 2020 were retrospectively studied. Stone-free rate (SFR) was evaluated on postoperative day (POD) 90 by noncontrast CT (NCCT) or ultrasound and kidney, ureter, and bladder radiograph (KUB) for each renal unit. Surgical complications based on Clavien-Dindo classification during the 90 days of follow-up were recorded. Sample size was calculated for a power of 80% and a significance level of 0.05, assuming SFR of 20% for SWL and 50% for RIRS. Results: Thirty-three patients treated by SWL were compared with 36 patients treated by RIRS. Hospitalization time was longer in the RIRS group (4.18 vs 12.33 hours, p = 0.001). SFR and success rate were lower in SWL than RIRS group (24.2% vs 58.3%, p = 0.007 and 30.3% vs 72.2%, p = 0.004, respectively), using POD 90 NCCT in 81.8% and ultrasound and KUB in 18.2% of the SWL group and using POD 90 NCCT in 100% of the RIRS group. Minor complications (Clavien-Dindo < III) occurred in 11 of 36 (30.6%) patients submitted to RIRS and in 2 of 33 (6.1%) patients submitted to SWL group ( p = 0.025). Two patients (6.1%) of the SWL group had Clavien-Dindo IIIb complication owing to Steinstrasse and were submitted to ureteroscopy. Emergency room visits were similar between groups (6.1% vs 8.3%, p = 1.0). Conclusions: RIRS has better SFR, higher minor complications, and lower major complications than SWL for the treatment of RSFs after standard PCNL.