BACKGROUND: Functional dyspepsia (FD) is characterized by persistent and recurrent dyspeptic symptoms, such as postprandial fullness and epigastric pain. Although it is rarely severe or life-threatening, it can degrade the quality of life and cause social and economic issues. As symptoms often persist despite the treatment with conventional Western medicine, herbal medicine can be considered as an alternative for treating FD. Siho-sogan-san (SHS) is a traditional herbal formula prescribed for dyspepsia for hundreds of years. This protocol for a systematic review was designed to evaluate the safety and efficacy of SHS for the treatment of FD through a meta-analysis. METHODS: Studies will be searched from the following electronic databases up to March 2020: Embase, MEDLINE (via PubMED), Cochrane Central Register of Controlled Trials, Allied and Complementary Medicine Database, Korean Medical Database, KoreaMed, Korean Studies Information Service System, National Digital Science Library, Oriental Medicine Advanced Searching Integrated System, China National Knowledge Infrastructure Database, and Citation Information by Nii. Randomized controlled trials of SHS and herb-added SHS for treating FD will be selected in this review. The control groups of no-treatment, placebo, and conventional Western medicine will be compared with SHS for its efficacy. The synergetic effect of SHS with Western medicine will also be analyzed in comparison with conventional Western medicine alone. Two independent reviewers will collect the data and assess the risk of bias in individual studies. The total clinical effectiveness rate will be synthesized and evaluated as primary outcome. RESULTS: This systematic review will present an adequate clinical evidence of SHS for the treatment of FD based on specific parameters, including dyspepsia-related symptoms, gastric emptying, and adverse events. CONCLUSION: This study will provide evidence for the safety and efficacy of SHS for the treatment of patients with FD. REVIEW REGISTRY UNIQUE IDENTIFYING NUMBER:: reviewregistry952.