Objective: To report the outcomes of percutaneous nephrolithotomy (PCNL) in horseshoe kidneys (HSK) in 12 institutions worldwide and evaluate the impact of patient position during operation. Methods: We carried out a retrospective analysis of PCNL procedures performed between 2008 and 2018 in patients with HSK. Pre-, peri-, and postoperative data were collected, and a subgroup analysis was performed according to patient position. Success was defined as an absence of >4-mm fragments. Values of p < 0.05 were considered significant. Results: We analyzed 106 procedures. The transfusion, complication, and immediate success rates (ISRs) were 3.8%, 17.5%, and 54.7%, respectively. The final success rate (FSR) increased to 72.4% after a mean of 0.24 secondary procedures. Logistic regression showed that higher body mass index (BMI) and stone size were significantly associated with residual fragments ≥4 mm. Sixty-seven patients (63.2%) were treated in prone and 39 (36.8%) in supine position. The prone group had a significantly higher BMI than the supine group (30.1 vs 27.7, p = 0.024). The transfusion, complication, and ISRs between the prone and supine groups were 4.5% vs 2.6% (p = 0.99), 16.9% vs 18.4% (p = 0.99), and 52.5% vs 69.2% (p = 0.151), respectively. Surgical time was significantly longer in the prone group (126.5 vs 100 minutes, p = 0.04). Upper pole was the preferred access in 80.3% of the prone group and 43.6% of the supine group (p < 0.001). The prone group had significantly more Clavien 2 complications than the supine (p = 0.013). The FSR in the prone and supine groups increased to 66.1% and 82.1% after 0.26 and 0.21 secondary procedures, respectively. No complications higher than Clavien 3 occurred. Conclusion: PCNL in patients with HSK is safe and effective with a low complication rate. Higher BMI and stone size negatively impacted outcomes. Supine PCNL may be an option for treating kidney stones in patients with HSK.