This study aims to test the feasibility of a randomised clinical trial to evaluate how acupuncture affects atopic dermatitis (AD) symptoms and quality of life and to explore potential biomarkers that may be associated with AD. It is a sham-controlled trial in which 30 eligible patients will be randomly allocated in a 1 : 1 : 1 ratio to one of three groups: verum acupuncture (VA) group 1 (3 times weekly for 4 weeks); VA group 2 (twice weekly for 4 weeks); or sham acupuncture group (SA; twice weekly for 4 weeks). SA will consist of nonpenetrating acupuncture. Outcome measures will include the Visual Analogue Scale for itch, SCORing Atopic Dermatitis, and Eczema Area and Severity Index to evaluate AD symptoms improvement along with the Patient Oriented Eczema Measure and Dermatology Life Quality Index to assess quality of life. Measures will be collected at baseline, once weekly during the treatment period, and after a 4-week follow-up period. Blood collection will be at baseline and 4 and 8 weeks after treatment and compared with healthy controls. Illumina sequencing will be used to profile microRNA expression in each group to explore candidate microRNA biomarkers for specific effects of acupuncture in patients with AD. This trial is registered via US National Institutes of Health Clinical Trials registry (ClinicalTrials.gov) on 15 July 2016, identifier: NCT02844452.