Vitamin D is a cofactor responsible for autoimmune disorders. There is no agreement in the studies investigating the association between vitamin D and fibromyalgia. This study aims to combine the conflicting results of the primary studies which compared these patients with control groups regarding the serum concentration of vitamin D. This meta-analysis has been designed based on PRISMA guidelines. Relevant keywords were searched in PubMed, Science direct, Scopus, Cochrane, and Google scholar and primary studies were selected. After screening the eligible studies according to inclusion/exclusion criteria, we investigated the risk of bias in the selected studies and also the heterogeneity between the primary results using Cochrane (Q) and I-squared (I2) indices. The primary results were combined using inverse variance method and Cohen statistics as well as a random effects model. Publication bias was assessed using Egger test. Sensitivity analysis was applied to investigate the influence of each primary study on the final result of the meta-analysis. Suspected factors in the heterogeneity were assessed using meta-regression models. We entered 12 eligible studies in the meta-analysis including 851 cases compared with 862 controls. The standardized mean difference of Vitamin D between the two groups was −0.56 (95% confidence interval: −1.05, −0.08). Our meta-analysis showed that vitamin D serum levels of patients with fibromyalgia was significantly lower than that of control group.