Acupuncture has been used as a therapy for several thousand years and is now being used as an alternative treatment for many medical conditions. It offers multiple applications. Its primary use includes alleviation of pain, reduction of inflammation and improvement of sleep disturbances. It is one of the first complementary and alternative medicine modalities to be incorporated in an integrative approach to care. However, the mechanism of therapeutic effects with acupuncture is still unclear and the theory underlying acupuncture is still controversial. Now biomedical engineering is applied to research the mechanism of therapeutic effects with acupuncture. In this article, the newest methods including electroencephalogram, Functional magnetic resonance imaging, Positron emission tomography, which was used to obtain information from the nervous system to determine how acupuncture works have been surveyed. Most of the methods show the acupuncture at acupoint induces specific patterns of brain activity, and these patterns may relate to the therapeutic effects of acupuncture.