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Objective Observational studies have shown that circulating vitamin D (VitD) deficiency is associated with atherogenic lipid patterns among polycystic ovary syndrome (PCOS) patients. However, interventional studies have shown inconsistent results. The aim of this meta-analysis was to investigate how VitD supplementation influences lipid indices in PCOS patients. Methods The authors searched four electronic databases through August 2019 to identify randomized controlled trials (RCTs) that assessed the effect of VitD intervention on serum lipids among PCOS patients. Mean differences were generated for statistical evaluation. Results We included eight studies and performed nine comparisons across 467 participants. VitD supplementation reduced serum triglyceride levels (−11.88 mg/dL; 95% confidence interval [CI]: −17.03 to −6.73), total cholesterol (−9.09 mg/dL; 95% CI: −14.90 to −3.29), low-density lipoprotein cholesterol (−5.22 mg/dL; 95% CI: −10.32 to −0.13), and very-low-density lipoprotein cholesterol (−2.43 mg/dL; 95% CI: −3.69 to −1.17) compared with no VitD supplementation. However, high-density lipoprotein cholesterol levels showed no differences with or without VitD supplementation (−0.39 mg/dL; 95% CI: −1.39 to 0.61). Conclusions VitD supplementation improved serum lipid levels among PCOS patients, but serum high-density lipoprotein cholesterol levels were not changed. VitD intervention might benefit PCOS patients who are at high risk of an atherogenic lipid profile.