We investigated the effect of probiotic supplementation on inflammatory bowel disease (IBD) by meta-analysis. We included 30 studies to assess the effect of probiotic administration. We estimated the effect size using standardized mean difference, and we evaluated the statistical heterogeneity of the effect size using Cochran's Q test, followed by meta-ANOVA and meta-regression analysis to explain the heterogeneity of the effect size using a mixed-effects model. We conducted Egger's linear regression test to evaluate publication bias. Among the factors evaluated, colon length and myeloperoxidase showed the greatest Q statistic and I2 index, respectively. Colon length, transforming growth factor-β, IL-10, superoxide dismutase, and glutathione showed positive effect sizes in the fixed- and random-effects models. The others (spleen weight, tumor necrosis factor α, IL-1β, IL-6, IL-12, IL-17, IFN-γ, disease activity index, thiobarbituric acid reactive substances, nitric oxide, myeloperoxidase, malondialdehyde, histological score, and macroscopic inflammatory score) showed negative effect sizes in the fixed- and random-effects models. Probiotics showed a significant effect on all investigated factors, except IL-10. In meta-ANOVA and meta-regression analysis, Lactobacillus paracasei was the most effective probiotic for colon length. Lactobacillus paracasei, Lactobacillus reuteri, Lactobacillus fermentum, and a mixture of Lactobacillus bulgaricus and Saccharomyces boulardii (LC + SB) were effective for colon length, tumor necrosis factor α, IL-6, IL-10, IFN-γ, and disease activity index. Lactobacillus rhamnosus was most effective for IL-10 and IFN-γ. Dietary probiotics are effective in improving the symptoms of IBD. Although the results of this meta-analysis had some limitations due to a lack of animal experiments, they will be meaningful to people with IBD.