Acupuncture analgesia is a traditional treatment with a long history, although it lacks scientific evidence. It is reportedly associated with the central nervous system, including various brain regions, from the cortices to the brain stem. However, it remains unclear whether the distributed regions behave as a single unit or consist of multiple sub-units playing different roles. Magnetoencephalography is a neuroimaging technique that can measure the oscillatory frequency of neural signals and brain regions. The frequency band of neural signals allows further understanding of the characteristics of the acupuncture-related neural systems. This study measured resting-state brain activity using magnetoencephalography in 21 individuals with chronic pain before and after acupuncture treatment. The subjective level of pain was assessed using a visual analog scale, and brain activity was compared to identify the brain regions and the frequencies associated with acupuncture analgesia. Here, we categorized the changes in resting-state brain activity into two groups: low-frequency oscillatory activity (<3 Hz) in the left middle occipital and right superior partial lobule and high-frequency oscillatory activity (81-120 Hz) on both sides of the prefrontal, primary sensory, and right fusiform gyri. These findings suggest that acupuncture analgesia influences two or more sub-units of the neural systems, which helps us understand the neural mechanisms underlying acupuncture analgesia.