The objective of this study is to assess the safety and efficacy of the flank position in percutaneous nephrolithotomy (PCNL). We searched PubMed, Embase, SCOPUS, the Cochrane database libraries, and the Chinese Biomedical Literature Database, and randomized controlled trials (RCTs) assessing PCNL in flank position are included in this meta-analysis. The related trials met the inclusion criteria were analyzed using RevMan 5.4. Seven randomized controlled trials were included, involving a total of 587 patients. We found that there was a lower decrease in hemoglobin levels in the flank position group compared to prone-position group (mean difference [MD] = − 0.15, 95% confidence interval (CI) − 0.22 to − 0.08, P < 0.00001). Moreover, our meta-analysis demonstrated no significant differences between groups regarding stone-free rate (relative risk [RR] = 1.00, 95% CI 0.93 to 1.06, P = 0.92), operative time(MD = 0.76, 95% CI − 5.31 to 6.83, P < 0.00001), hospital stay (MD = 0.03, 95% CI − 0.32 to 0.32, P < 0.00001), and complications Clavien grade I (RR = 1.01, 95% CI 0.98 to 1.05, P = 0.54), Clavien grade II (RR = 1, 95% CI 0.97 to 1.02, P = 0.78), and Clavien grade III (RR = 1, 95% CI 0.98 to 1.03, P = 0.77). The use of flank position for PCNL is associated with reduced hemoglobin change without an increase in complications. This positioning technique can be considered safe for patients with nephrolithiasis and may be particularly suitable for high-risk individuals such as those who are obese or have decreased cardiopulmonary function. However, further randomized trials are needed to confirm these findings.