This meta-analysis was performed to resolve the inconsistencies regarding resistin and follistatin levels in women with polycystic ovary syndrome (PCOS) by pooling the available evidence. A systematic literature search using PubMed and Scopus was carried out through November 2020 to obtain all pertinent studies. Weighted mean differences (WMDs) with corresponding 95% confidence intervals (CIs) were calculated to evaluate the strength of the association between the levels of resistin and follistatin with PCOS in the overall and stratified analysis by obesity status. A total of 47 publications, 38 for resistin (2424 cases; 1906 controls) and 9 studies for follistatin (815 cases; 328 controls), were included in the meta-analysis. Resistin levels were significantly higher in PCOS women compared with non-PCOS controls (WMD = 1.96 ng/ml; 95%CI = 1.25–2.67, P≤0.001) as well as in obese PCOS women vs. obese controls, and in non-obese PCOS women compared with non-obese controls, but not in obese PCOS vs. non-obese PCOS patients,. A significantly increased circulating follistatin was found in PCOS patients compared with the controls (WMD = 0.44 ng/ml; 95%CI = 0.30–0.58, P≤0.001) and in non-obese PCOS women compared with non-obese controls and in obese PCOS women vs. obese controls, but, no significant difference in follistatin level was observed in obese PCOS compared with non-obese PCOS women. Significant heterogeneity and publication bias was evident for some analyses. Circulating levels of resistin and follistatin, independent of obesity status, are higher in women with PCOS compared with controls, showing that these adipokines may contribute to the pathology of PCOS.