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Abstract Background Atopic Dermatitis is a chronic relapsing eczematous skin disease with increasing prevalence and rising costs. It has a clear impact on a patient's quality of life. Many patients are worried about the use of usual care techniques, such as corticosteroids and antihistamine due to the widespread fear of adverse effects. Complementary and alternative medical approaches have been employed to relieve symptoms of Atopic Dermatitis. Hwangryunhaedoktang is among the most strongly preferred and widely used herbal medicines for Atopic Dermatitis in Korea, as it causes very few serious adverse effects. We aim to establish basic clinical efficacy and safety data for Hwangryunhaedoktang, which is approved as an herbal medication by the Korean Food and Drug Administration, in adult patients with Atopic Dermatitis. Methods/Designs This study is a randomised, double blind, placebo-controlled, two-centre trial with two parallel arms (Hwangryunhaedoktang and a placebo). The diagnosis of Atopic Dermatitis will be made according to the criteria of Hanifin and Rajka by two different Oriental medicine doctors. We will include participants experiencing typical conditions of intermittent or continuous Atopic Eczema for six or more months. Participants will receive Hwangryunhaedoktang or a placebo-drug for eight weeks. The total duration of each arm is eleven weeks. Each participant will be examined for signs and symptoms of Atopic Dermatitis before and after taking medication. A follow-up to evaluate the maintenance of safety will be performed two weeks after the final administration of medication. Discussion This trial will utilize high quality trial methodologies in accordance with consolidated standards of reporting trials guidelines. It will provide evidence for the clinical efficacy and safety evaluation of Hwangryunhaedoktang in adult patients with Atopic Dermatitis. Moreover, we will also employ health-related quality of life questionnaires to assess the changes in quality of life. Trial registration Current Controlled Trials ISRCTN26218532