Electro-acupuncture, an innovative adaptation of traditional acupuncture, combines electrical stimulation with acupuncture needles to enhance therapeutic effects. While acupuncture is widely used, its biological mechanisms remain incompletely understood. Recent research has explored the neurophysiological aspects of acupuncture, particularly through functional magnetic resonance imaging (fMRI) to investigate its effects on brain activity. In this systematic review, we conducted an extensive search for randomized clinical trials examining electro-acupuncture effects measured by fMRI. We employed strict eligibility criteria, quality assessment, and data extraction. Five studies met our inclusion criteria and were analyzed. The selected studies investigated electro-acupuncture in various medical conditions, including carpal tunnel syndrome, fibromyalgia, Crohn's disease, irritable bowel syndrome, and obesity. Notably, electro-acupuncture was found to modulate brain activity and connectivity in regions associated with pain perception, emotional regulation, and cognitive processing. These findings align with the holistic approach of traditional Chinese medicine, emphasizing the interconnectedness of body and mind. In carpal tunnel syndrome, electro-acupuncture at both local and distal sites showed neurophysiological improvements, suggesting distinct neuroplasticity mechanisms. In fibromyalgia, somatosensory electro-acupuncture correlated with reduced pain severity, enhanced brain connectivity, and increased gamma-aminobutyric acid levels. For Crohn's disease, electro-acupuncture influenced the homeostatic afferent processing network, potentially mitigating gut inflammation. Electro-acupuncture for irritable bowel syndrome led to decreased activity in the anterior cingulate cortex, offering pain relief, while electro-acupuncture for obesity impacted brain regions associated with dietary inhibition and emotional regulation. This systematic review provides evidence that electro-acupuncture can positively impact a range of medical conditions, possibly by modulating brain activity and connectivity. While the quality of the reviewed studies is generally good, further research with larger sample sizes and longer-term assessments is needed to better understand the mechanisms and optimize electro-acupuncture protocols for specific health conditions. The limited number of studies in this review emphasizes the need for broader investigations in this promising field. The research protocol was registered in PROSPERO (CRD42023465866).