Observational studies have indicated an inverse association between vitamin D levels and the risk of diabetes, yet evidence from population interventions remains inconsistent. PubMed, EMBASE, Cochrane Library and ClinicalTrials.gov were searched up to September 2017. Data from studies regarding serum 25(OH)D, fasting blood glucose (FBG), hemoglobin A1c (HbA1c), fasting insulin and homeostasis model assessment of insulin resistance (HOMA-IR) were pooled. Twenty studies (n = 2703) were included in the meta-analysis. Vitamin D supplementation resulted in a significant improvement in serum 25(OH)D levels (weighted mean difference (WMD) = 33.98; 95%CI: 24.60–43.37) and HOMA-IR (standardized mean difference (SMD) = −0.57; 95%CI: −1.09~−0.04), but not in other outcomes. However, preferred changes were observed in subgroups as follows: short-term (WMDFBG = −8.44; 95%CI: −12.72~−4.15), high dose (WMDFBG = −8.70; 95%CI: −12.96~−4.44), non-obese (SMDFasting insulin = −1.80; 95%CI: −2.66~−0.95), Middle Easterners (WMDFBG = −10.43; 95%CI: −14.80~−6.06), baseline vitamin D deficient individuals (WMDFBG = −5.77; 95%CI: −10.48~−1.05) and well-controlled HbA1c individuals (WMDFBG = −4.09; 95%CI: −15.44~7.27). Vitamin D supplementation was shown to increase serum 25(OH)D and reduce insulin resistance effectively. This effect was especially prominent when vitamin D was given in large doses and for a short period of time, and to patients who were non-obese, Middle Eastern, vitamin D deficient, or with optimal glycemic control at baseline.