BACKGROUND: Functional dyspepsia (FD) refers to the presence of one or more gastrointestinal symptoms including postprandial fullness, epigastric pain, burning, and early satiety without an organic explanation for chronic symptoms. FD causes considerable discomfort in patients and affects their everyday activity and productivity. Because most conventional treatments have limited efficacy, numerous patients seek alternatives such as herbal medicines. In this proposed study, we will conduct a clinical trial of an herbal drug, Banha-sasim-tang (BST). Furthermore, participants will be limited to those classified as having an excess pattern by using an instrument of pattern identification for FD to determine the efficacy of BST in a specific subset of patients. METHODS: This randomized, blinded, parallel-group clinical trial of BST versus placebo will consist of 4 weeks of oral administration of BST or placebo and a 4-week follow-up period. The Korean version of the symptom-based questionnaire of the Nepean Dyspepsia Index (NDI-K) will be used as the primary outcome measure. Secondary outcome measures will include the quality-of-life (QoL) evaluation from the NDI-K, the FD-related QoL (FD-QoL) scale, assessment of gastric myoelectrical dysrhythmias (GMA), and a Visual Analog Scale (VAS) analysis. DISCUSSION: The results of this trial are expected to provide relevant evidence demonstrating that BST can be used as an effective treatment in a specific subset of FD subjects. TRIAL REGISTRATION: KCT 0002013 . Registered at Clinical Research Information Service in the Republic of Korea on 18 August 2016.