BACKGROUND: Functional dyspepsia (FD) is a functional gastrointestinal disorder. Evidence suggests that disturbance of the gastrointestinal microbiota may be implicated in FD. We performed a systematic review and meta-analysis to examine the efficacy of prebiotics and probiotics for FD. METHODS: MEDLINE, EMBASE, and the Cochrane Controlled Trials Register were searched (through September 2018). Randomized controlled trials (RCTs) that recruited adults with FD and that compared prebiotics, probiotics, or synbiotics with placebo or no therapy were eligible. Eligibility assessment and data extraction were performed by two independent researchers. Dichotomous symptom data were pooled to obtain a relative risk (RR) with a 95% confidence interval (CI) of remaining symptomatic after therapy. Continuous data were pooled using a standardized or weighted mean difference with a 95% CI. RESULTS: The search strategy identified 1062 citations. Five RCTs were eligible for inclusion. The RR of FD symptoms improving with probiotics or probiotics vs placebo was 1.15 (95% CI 1.01-1.30). Probiotics and prebiotics had beneficial effects on symptom scores of FD. Data for synbiotics in the context of FD were sparse, and no definite conclusions could be drawn. ETHICS AND DISSEMINATION: This study belongs to the category of systematic reviews, not clinical trials. Therefore, it does not require ethical approval. The results of this study will be published in influential international academic journals related to this topic. CONCLUSION: Probiotics and prebiotics seemed to be effective treatments for FD, although the individual species and strains that are the most beneficial remain unclear. Using only probiotics failed to improve the symptoms of FD. Further evidence is required before the role of probiotics, prebiotics, and synbiotics in FD can be fully understood.