BACKGROUND: Functional dyspepsia (FD) is a common functional gastrointestinal disorder characterized by recurrent dyspeptic symptoms. Yukgunja-tang (YGT) is a traditional herbal formula that has been used for treating FD. This systematic review protocol aims to provide a guideline for investigating the efficacy and safety of YGT in the treatment of FD. METHODS: The following databases will be searched from their inception until July 2018: Medline (via PubMed), EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), Allied and Complementary Medicine Database (AMED), KoreaMed, National Digital Science Library (NDSL), Korean Medical Database (KMbase), Oriental Medicine Advanced Searching Integrated System (OASIS), Korean Studies information Service System (KISS), China National Knowledge Infrastructure Database (CNKI), and Citation Information by Nii (CiNii). Randomized controlled trials (RCTs) that used YGT or modified YGT for treating FD will be included. The control groups in these RCTs will include placebo, no-treatment waiting, and conventional western medicine groups. Trials testing YGT as an adjunct to western medicine for synergistic effect will also be included. The main outcome will be the total clinical efficacy rate. Data extraction and risk of bias assessment will be performed by two independent assessors. RevMan V.5.3 will be used for data analysis. RESULTS: This study will provide a high-quality synthesis of current evidence of YGT for FD from several aspects including dyspepsia-related symptoms, quality of life and adverse events. CONCLUSION: The conclusion of our systematic review will provide evidence to judge whether YGT is an effective intervention for patient with FD. ETHICS AND DISSEMINATION: The protocol does not need ethics approval because identifying information of the participants will not be revealed. The systematic review will be published in a peer-reviewed journal and disseminated electronically and in print. TRIAL REGISTRATION NUMBER: PROSPERO CRD42018090139.