We conducted a meta-analysis to evaluate the effects of probiotics and prebiotics on the immune response to influenza vaccination in adults. We conducted a literature search of Pubmed, Embase, the Cochrane Library, the Cumulative Index to Nursing and Allied Health (CINAHL), Airiti Library, and PerioPath Index to Taiwan Periodical Literature in Taiwan. Databases were searched from inception to July 2017. We used the Cochrane Review risk of bias assessment tool to assess randomized controlled trial (RCT) quality. A total of 20 RCTs comprising 1979 adults were included in our systematic review. Nine RCTs including 623 participants had sufficient data to be pooled in a meta-analysis. Participants who took probiotics or prebiotics showed significant improvements in the H1N1 strain seroprotection rate (with an odds ratio (OR) of 1.83 and a 95% confidence interval (CI) of 1.19-2.82, p = 0.006, I² = 0%), the H3N2 strain seroprotection rate (OR = 2.85, 95% CI = 1.59-5.10, p < 0.001, I² = 0%), and the B strain seroconversion rate (OR = 2.11, 95% CI = 1.38-3.21, p < 0.001, I² = 0%). This meta-analysis suggested that probiotics and prebiotics are effective in elevating immunogenicity by influencing seroconversion and seroprotection rates in adults inoculated with influenza vaccines.