The aim of the present meta-analysis was to evaluate the effect of vitamin D supplementation on patients with polycystic ovary syndrome (PCOS). A literature search was performed to identify all of the relevant studies comparing the effect of vitamin D supplementation with placebo in PCOS patients, in the PubMed, Embase and Web of Science databases. All statistical analyses were performed on case-control studies using Review Manager 5.3 software, provided by the Cochrane Collaboration. A total of 11 studies involving 483 participants were included in the current meta-analysis. Vitamin D supplementation appeared to lead to an improvement in the levels of total testosterone [weighted mean differences (WMD) = -0.10, 95% CI (-0.18, -0.02)], homeostasis model assessment of insulin resistance [WMD = -0.44, 95% CI (-0.86, -0.03)], homeostasis model assessment of β-cell function [WMD = -16.65, 95% CI (-19.49, -13.80)], total cholesterol [WMD = -11.90, 95% CI (-15.67, -8.13)] and low-density lipoprotein-cholesterol [WMD = -4.54; 95% CI (-7.29, -1.80)]. The results failed to show a positive effect of vitamin D supplementation on the body mass index, dehydroepiandrosterone sulfate, triglyceride levels or high-density lipoprotein-cholesterol. In conclusion, the data from the available randomized controlled trials (RCTs) suggested vitamin D supplementation reduced insulin resistance and hyperandrogenism, as well improving the lipid metabolism of patients with PCOS to an extent. Further high-quality RCTs from a variety of regions in the world are required to determine the effectiveness of vitamin D supplementation in PCOS patients, and to determine a suitable dose and unit of vitamin D.