BackgroundType-2 diabetes has become a major disease and is known to seriously impair people’s health worldwide. Prediabetes includes impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and is the most critical period for preventing type-2 diabetes, as it can be identified and reversed. Studies in the past decade have indicated that acupuncture and Chinese herbal medicine may be beneficial for treating prediabetes. However, a randomized controlled trial (RCT) should be conducted to obtain more clinical evidence on this topic.Methods/designAn RCT will be implemented in this study, using a72-week study period (24 weeks for the intervention and 48 weeks for follow-up). Participants will be recruited from the Fifth Affiliated Hospital of Guangzhou Medical University in China. Eighty participants will be randomized to the treatment group (acupuncture plus herbal medicine and health education) or the control group (health education only), 40 participants in each. People included in this study must have been diagnosed with prediabetes using Western medicine criteria. The endpoint indices include the incidence of diabetes mellitus and the reversion rate. The primary outcome is fasting plasma glucose (FPG) level, 2-h plasma glucose (2-hPG) level after a 75-g oral glucose tolerance test (OGTT), and glycosylated hemoglobin (HbA1c) level. Secondary outcomes include the following: Body Mass Index (BMI); hemorheology, including shear rates of whole-blood viscosity and plasma viscosity. Safety indices include hepatic (ALT, AST) and renal function (BUN, Cr) and records of adverse events, including diarrhoea, colds, pharyngitis, and sleep disorders. Quality control will be implemented, including quality control of the laboratory, researchers, participants, investigational drugs, data and documents, occurrence of bias, supervision, among others, according to uniform standard operating procedures (SOPs) which have been established by the Good Clinical Practice (GCP) office of the Fifth Affiliated Hospital of Guangzhou Medical University.DiscussionThe aim of this study is to evaluate the efficacy and safety of acupuncture paired with herbal medicine for the treatment of patients with prediabetes.Trial registrationChinese clinical trials register ChiCTR-INR-16008891. Registered on 23 July 2016.Electronic supplementary materialThe online version of this article (doi:10.1186/s13063-017-2014-4) contains supplementary material, which is available to authorized users.