Introduction <p>Fibromyalgia (FM) is a condition of generalized musculoskeletal pain, associated with fatigue, autonomic dysfunction, and sleep disorders. Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique, tested in several diseases, including FM and depending on the parameters used, tDCS can reach several brain neural networks, including the central processing network of the pain. Another therapy that promotes analgesia is manual therapy (MT) which is defined as a set of techniques that uses the hands as the main therapeutic agents. Evidence indicates that MT, applied at points along the vagus nerve (VN), may improve pain in patients with chronic pain. This study will examine the immediate and late effects of tDCS associated with MT on the VN pathway in pain in women with FM.</p> Methods <p>This is a controlled, randomized, double-blind clinical trial with intention-to-treat analysis that will follow the guidelines of CONSORT (Consolidated Reporting Standards). The study will consist of 30 women diagnosed with FM who will be randomly allocated to the experimental group (tDCS 2 mA active for 20 min associated with MT) or to the control group (tDCS for 20 min associated with MT sham) and will receive daily sessions of treatment for 5 days. Outcome measures will occur at the beginning of the study, after the first visit, at the end of treatment, and 30 days after the end of treatment.</p> Discussion <p>The search for therapies to improve pain in FM is quite challenging, mainly due to the lack of knowledge about its etiopathogenesis and the complexity of symptoms that are associated with it. Thus, this clinical trial may result in an important advance for the rehabilitation of FM patients.</p> Clinical trial registration <p>U1111-1264-9863</p>