Purpose To assess the efficacy and safety of berberine on reproductive endocrine and metabolic outcomes in women with polycystic ovary syndrome (PCOS). Methods PubMed (from 1950), the Cochrane Library, the CNKI (from 1979), the VIP (from 1989), and the Wanfang Data (from 1990) and the reference lists of the retrieved articles were searched for randomized controlled trials in human beings with the search terms including “polycystic ovary syndrome/PCOS” and “berberine/BBR/Huangliansu (in Chinese)/Xiao bojian (in Chinese)” till 30 May 2019. Relevant indicators were collected and the data were analyzed by using RevMan 5.3 software. Results Eventually, a total of 12 randomized controlled trials were included in this systematic review. Our study suggested that berberine had similar live birth rates compared with placebo or metformin and lower live birth rates (RR: 0.61, 95% CI: 0.44 to 0.82) compared with letrozole. There was a significant difference between berberine and placebo and between berberine and no treatment in terms of decreasing total testosterone and luteinizing hormone to follicle-stimulating hormone (LH/FSH) ratio (8 RCTs, 577 participants, MD: −0.34, 95% CI: −0.47 to −0.20; 3 RCTs, 179 participants, MD: −0.44, 95% CI: −0.68 to −0.21, respectively). Berberine was associated with decreasing total cholesterol (3 RCTs, 201 participants; MD: −0.44, 95% CI: −0.60 to −0.29), waist circumference (3 RCTs, 197 participants, MD: −2.74, 95% CI: −4.55 to −0.93), and waist-to-hip ratio (4 RCTs, 258 participants, MD: −0.04, 95% CI: −0.05 to −0.03) compared with metformin, but not with improved BMI (4 RCTs, 262 participants, MD: −0.03, 95% CI: −0.46 to 0.39). Berberine did not increase the incidence of gastrointestinal adverse events (3 RCTs, 567 participants, RR: 1.01, 95% CI: 0.76 to 1.35) or serious events during pregnancy (RR: 0.98, 95% CI: 0.70 to 1.37) compared with placebo. Conclusion This review found no solid evidence that berberine could improve live birth or other clinical outcomes in women with PCOS. However, berberine appeared to be more efficacious for improving insulin resistance and dyslipidemia and decreasing androgen levels and LH/FSH ratio in women with PCOS when compared with metformin.