BackgroundThis study aims to assess the efficacy and safety of geonchildan, a Korean traditional herbal medicine, for patients with active rheumatoid arthritis (RA) and evaluate the feasibility of a large-scale confirmatory clinical trial.Methods/designThis is a randomized, double-blind, placebo-controlled, parallel two-arm pilot trial in Seoul, Korea. Altogether, 30 patients diagnosed with RA for at least 3 months and with a Disease Activity Score for 28 joints (DAS28) ≥ 3.2 will be enrolled. Participants are randomly assigned to one of two groups, the experimental group or the placebo group, in a 1:1 ratio and will make four scheduled visits. The participants will be administered geonchildan or a placebo three times per day for 12 weeks. The change in DAS28 will be examined as the primary efficacy outcome. The secondary efficacy outcomes include the proportion of patients achieving ACR20, ACR50, ACR70, and EULAR responses; the DAS28 sub-items; the consumption of medication; Korean Health Assessment Questionnaire scores; inflammatory parameters; and the Korean medical diagnostic pattern indicator. Adverse events and laboratory test results will be recorded to evaluate safety. The process, resources used, and management of the study will also be assessed to determine the feasibility of a large-scale trial.DiscussionThis is the first clinical trial to explore the efficacy and safety of geonchildan in patients with active RA. If the superiority of geonchildan versus the placebo is demonstrated and the study design is feasible, this study could form the foundation for a large-scale clinical trial. The results will be published in a peer-reviewed journal.Trial registrationClinical Research Information Service, KCT0001943. Registered on 14 June 2016.Electronic supplementary materialThe online version of this article (10.1186/s13063-018-2849-3) contains supplementary material, which is available to authorized users.