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Background: Functional dyspepsia (FD) is a prevalent gastric disorder that is difficult to manage due to lack of satisfactory treatments. Acupuncture has been studied with regard to the rising need for treating FD, but the mechanism verifying its efficacy has not yet been fully revealed. The aim of this study is to explore the efficacy and mechanism of acupuncture for FD compared with a sham group. Methods/design: We describe a proposal for a randomized, assessor-blind, sham-controlled trial with 70 eligible participants who will be randomly allocated either into an acupuncture or a sham group. Participants in the acupuncture group will receive 10 sessions of real acupuncture treatment and those in the sham group will be treated with identical sessions using a Streitberger needle. Functional magnetic resonance imaging (fMRI) and metabolomics studies will be implemented before and after 4 weeks of treatment to investigate the mechanism of acupuncture. The primary outcome is a proportion of responders with adequate symptom relief and the secondary outcomes include the Nepean Dyspepsia Index - Korean version, Functional Dyspepsia-Related Quality of Life questionnaire, Ways of Coping Questionnaire, Coping Strategies Questionnaire, perception of bodily sensation questionnaire, State-Trait Anxiety Inventory, and the Center for Epidemiological Studies - Depression Scale. The outcomes will be evaluated before and after the treatment. Discussion: This is the first large-scale trial evaluating the efficacy and mechanism of acupuncture with fMRI and metabolomic methods. We will compare real acupuncture with the Streitberger sham needle to verify the specific effect of acupuncture. The results of this trial are expected to be relevant evidences affecting policy and decision-makers associated with routine healthcare. Trial Registration: ClinicalTrials.gov Identifier: NCT02358486 . Date of Registration: 21 January 2015. [ABSTRACT FROM AUTHOR]