Insomnia seriously affects quality of life and efficiency of work. Magnetic stimulation technique has outstanding advantages in stimulation of cranial nerve and deep nerve tissue. However, the effect of magnetic stimulation on insomnia is not clear. In this study, eighteen subjects (nine healthy subjects and nine insomniacs) were selected and magnetic stimulation at acupuncture points (acupoints) were carried out to the insomnia subjects. 64-channel electroencephalography (EEG) signals under different states (healthy subjects’ resting state, insomnia subjects’ resting state before and after magnetic stimulation) were recorded. Based on the synchronization of EEG signal, brain functional networks were constructed and analyzed. The results showed that compared with those of healthy subjects, the brain functional connections of insomniacs were increased at EEG β and γ bands. After magnetic stimulation, insomniacs’ brain functional connections at EEG β and γ bands were decreased. The results indicated that magnetic stimulation at acupoints could improve the brain functional networks of insomniacs. .