Functional dyspepsia (FD) is a common functional gastrointestinal disorder in clinical practice. Due to its long-term natural history, FD significantly impacts patients' quality of life and imposes a heavy social burden. Existing evidence suggests that acupuncture can effectively alleviate FD symptoms and is safe for treatment. However, current studies still face fragmented evidence regarding acupoint combinations, standardized procedures, and subtype interventions. Moreover, the existing clinical guidelines for FD do not provide specific recommendations on acupuncture treatment. To address the series of clinical issues faced by acupuncture in treating FD and to offer a scientific and standardized clinical protocol for acupuncture in FD treatment, the establishment of the "Clinical Practice Guidelines for Acupuncture Treatment of Functional Dyspepsia" was initiated by the Wangjing Hospital of the China Academy of Chinese Medical Sciences. This protocol systematically introduces the background, basic steps, working group members and their responsibilities, scope of application, the collection and determination of clinical issues and outcome indicators, evidence retrieval and evaluation methods, formulation of recommendations, external review and approval of recommendations, release and updating of the final draft, and the processes of promotion and implementation.