Background: Numerous randomized controlled trials on the effects of electro-acupuncture have been conducted to treat dysphagia as a sequela of stroke. However, the normal physiological mechanisms of swallowing and the pathological mechanisms of dysphagia are not fully understood. The purpose of this study is to investigate whether lateralization of the human swallowing motor cortex excitability in healthy subjects will be influenced by electro-acupuncture to Lianquan (CV 23) and Fengfu (GV 16), which may provide insight into the pathological mechanisms of dysphagia after stroke. Methods: We designed a single-blind, randomized, sham-controlled trial in which 40 healthy subjects will be recruited. Subjects will be randomized 1:1 into two groups: the electro-acupuncture group and the sham-control electro-acupuncture group. The swallowing motor cortex will be located in both groups using a neuroimaging navigation system. Then left and right cortical stimulation will be measured by transcranial magnetic stimulation (TMS) before and after electro-acupuncture or sham electro-acupuncture. The electro-acupuncture or sham electro-acupuncture interventions will last for 15 min. The primary outcome measure will be percent change in the resting motor threshold (RMT) of the mylohyoid. The secondary outcome measures will be the amplitude (mu V) and latency (ms) of the motor evoked potential (MEP) of the mylohyoid as a proxy for the TMS evoked potential. All outcomes will be measured at baseline and after the electro-acupuncture or sham electro-acupuncture treatment. Discussion: The aim of this trial is to explore whether lateralization of the human swallowing motor cortex excitability in healthy subjects is present, and to determine if electro-acupuncture to acupuncture points Lianquan (CV 23) and Fengfu (GV 16) will exert an effect on it under normal physiological conditions.