Abstract Purpose To compare the outcomes and complications of supine X-ray-free ultrasound-guided percutaneous nephrolithotomy (XG-PCNL) with fluoroscopy-guided (FG)-PCNL in both prone and supine positions. Methods This was a comparative study that included a prospective cohort and historical control groups. This study analysed 40 consecutive patients who undergone supine XG-PCNL between October 2019 and March 2020. The control groups were composed of historical control formed from the last 40 consecutive patients who underwent FG-PCNL in both supine and prone positions from our PCNL database from January 2018 and September 2019. Patients’ demographics, stone characteristics and intraoperative and postoperative outcomes were compared. Results A total of 120 patients were classified into the supine XG-PCNL, supine FG-PCNL, and prone FG-PCNL groups (each N = 40). They had similar baseline characteristics and initial stone burden. The supine XG-PCNL group had higher puncture attempts, nephrostomy tube placement, and longer surgery duration than both the supine and prone FG-PCNL groups. However, the stone-free rate was similar in all groups (85%, supine XG-PCNL; 72.5%, supine FG-PCNL; 77.5% prone FG-PCNL; p = 0.39). No significant difference was found in the complication rate and length of stay among the three groups. Conclusion Supine XG-PCNL is an alternative to both supine and prone FG-PCNL with similar efficacy and complication rates for kidney stone patients. This could be a good alternative to urological centres with no access to fluoroscopy.