For the treatment of large upper urinary stones percutaneous nephrolithotomy (PCNL) is generally considered the first choice, and Laparoscopic Stone Surgery (LSS) is an alternative. We aim to compare the efficiency and safety of PCNL with LSS, as far as the management of large upper urinary stones is concerned. A systematic search from Pubmed, Web of Science, Wiley Online Library and Elsevier was performed up to August 1, 2015 for the relevant published studies. After data extraction and quality assessment, meta-analysis was performed using the RevMan 5.3 software. 15 eligible trials evaluating LSS vs. PCNL were identified including 6 prospective and 9 retrospective studies with 473 patients undergoing LSS and 523 patients undergoing PCNL. Although LSS led to longer operative time (p = 0.01) and higher open conversion rate (p = 0.02), patients might benefit from significantly fewer overall complications (p = 0.03), especially lower bleeding rate (p = 0.02), smaller drop in hemoglobin level (p < 0.001), less need of blood transfusion (p = 0.01). The stone free rate was also higher for LSS compared with PCNL (p < 0.001) with less secondary/complementary procedure (p = 0.006). There was no significant difference in other demographic parameters between the two groups. Our data suggests that LSS turns out to be a safe and feasible alternative to PCNL for large upper urinary stones with less bleeding and higher stone free rate. Because of the inherent limitations of the included studies, further large sample prospective, multi-centric studies and randomized control trials should be undertaken to confirm our findings.