Abstract Background Atopic dermatitis (AD) is a common pruritic inflammatory skin disease with increasing prevalence. It can manifest with many different clinical phenotypes; however, in its chronic stage, hyperpigmentation, excoriation, lichenification, and dryness are the main symptoms. Jaungo comprises two herbs, Lithospermi radix and Angelica gigantis radix, and three carrier oils, and is an approved herbal ointment for xerosis cutis in Korea. In past studies, we demonstrated that Jaungo had anti-inflammatory and antiallergic activity in in vitro and in vivo AD models; however, there are few relevant randomized controlled clinical trials on Jaungo in AD. Methods/design A randomized, double-blind, placebo-controlled, single-center, phase IIa clinical trial was designed to investigate the safety, preliminary efficacy, and dose response of Jaungo in AD. The study protocol was approved by the Institutional Review Boards of the Kyung Hee University Korean Medicine Hospital (No. KOMCIRB-160617-HR-027) and the Korea Food and Drug Administration (No. 30907). The study aims to enroll 34 AD patients to be randomly distributed among three parallel groups: treatment 1, treatment 2, and the placebo group. Treatment group 1 applies Jaungo twice a day, while treatment group 2 applies Jaungo and the placebo ointment once a day, separately, and the placebo group applies the placebo ointment twice a day, for a total of 3 weeks each. Participants will be evaluated for eczema before and after the application of the ointments based on several parameters including the Eczema Area and Severity Index, the SCORing of Atopic Dermatitis Index, the Dermatology Life Quality Index, transepidermal water loss, total IgE level, eosinophil count, and IL-17, IL-22, and IFN-γ levels. Discussion The trial is currently ongoing and the enrollment of subjects has been initiated. There is an urgent need to develop a drug for the treatment of dry, hyperpigmented, scaly, and thickened skin in chronic-stage AD. This study will determine the efficacy and safety of Jaungo in AD, providing evidence for specific AD symptoms treated by Jaungo. Trial registration Clinical Trials.gov, identifier: NCT02900131 . Registered on 2 September 2016. Korea Clinical Research Information Service, identifier: KCT0002060 . Registered on 22 July 2016.