BACKGROUND: Functional dyspepsia (FD) is a common functional gastrointestinal disease with a high prevalence. However, due to the limitations of conventional Western treatments, such as acid suppressants, prokinetics, Helicobacter pylori eradication treatment, and antidepressants, the popularity of complementary and alternative medicine, such as acupuncture, is steadily increasing. We describe the methods that will be used to evaluate the effectiveness and safety of acupuncture as add-on therapies to conventional Western medications in patients with FD. METHODS AND ANALYSIS: A total of 12 English, Korean, and Chinese electronic databases will be searched by 2 researchers from their inception dates to December 2020. Randomized controlled trials assessing the effectiveness and safety of acupuncture as add-on therapies to conventional Western medications in patients with FD will be included. The primary outcome measure will be the symptom score of FD, and secondary outcome measures will be total effective rate, quality of life, level of gut peptide hormones, incidence of adverse events, and recurrence rate. Data analysis will be performed using the Review Manager version 5.3. The risk of bias of the included studies and the quality of evidence for the main findings will be evaluated using the Cochrane Collaborations risk of bias tool and the Grading of Recommendations Assessment, Development, and Evaluation approach, respectively. CONCLUSION: The findings of this review will provide evidence on the complementary effectiveness and safety of acupuncture for FD for clinicians, patients, and policy makers in decision making. OSF REGISTRATION NUMBER: DOI 10.17605/OSF.IO/MXREN (https://osf.io/mxren).