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Functional dyspepsia (FD) has a high prevalence rate. The dyspeptic symptoms are not easily cured despite the availability of various conventional Western medical treatments. Banha-sasim-tang (BST) is a traditional herbal medicine that has long been used for treating FD.The following databases will be searched from inception to January 2019: Medline via PubMed, the Cochrane Central Register of Controlled Trials, EMBASE, Allied and Complementary Medicine Database, National Digital Science Library, Korean Medical Database (KoreaMed), Oriental Medicine Advanced Searching Integrated System, Korean Studies Information Service System, China National Knowledge Infrastructure Database, and Citation Information by Nii. Randomized controlled trials (RCTs) that used BST or herbs-added BST for treating FD will be included in the systematic review. Control groups in these RCTs will be the placebo, no-treatment, and conventional Western medicine groups. RCTs that compared BST and Western medicine combination therapy with the conventional Western medicine will also be included in the systematic review to investigate the synergistic effect of BST and Western medicine. Data extraction and evaluation of risk of bias will be performed by 2 independent investigators. The primary outcome will be the total clinical effective rate and secondary outcomes will include gastrointestinal symptom scale, visual analog scale, FD-related quality of life, electrogastrography, plasma motilin, dyspepsia-related symptom score, gastric emptying, and adverse events. RevMan version 5.3 will be used for data integration and analysis.This systematic review will provide a high-quality integration of current evidence of BST for treating FD from several aspects including total clinical effective rate, dyspepsia-related symptoms, quality of life, and adverse events.This systematic review will provide evidence of the effectiveness and safety of BST on FD.Identifying information of the participants will not be revealed; hence, this protocol does not need ethical approval. The systematic review will be published in a peer-reviewed journal and disseminated electronically.PROSPERO CRD42019123285.