Recent advances in neuroendocrinology and immunology have provided an entry to understand acupuncture. Here, we highlight these progresses and use endometriosis as an example to provide a perspective in how to effectively engage acupuncture into modern biomedicine. Endometriosis is a common chronic inflammatory disease in which endometrial tissue progressively grows outside the uterine cavity and into the pelvic region, including the fallopian tubes and ovaries. Also, estrogen promotes the endometriosis progression through on-site inflammation. Current treatments for endometriosis involve hormonal therapy and surgical procedures, however, they both may induce several side effects. Several studies have shown that the administration of exogenous dopamine agonists can significantly suppress endometriosis progression. Acupuncture is multivalent in which it can simultaneously stimulate the secretion of endogenous dopamine to modulate the GnRH neuroendocrine pathway in CNS and the COX-2 inflammatory pathway in PNS. Hence, acupuncture can smoothly manage endometriosis without the side effects of exogenous dopamine. The endometriosis management by acupuncture provides us an example of how to incorporate acupuncture into current biomedical systems. Acupuncture may provide a convenient, physiological method to regulate the neuroendocrine system in an integrative, systematic means.