Objective The aim of the present work was to observe the activation/deactivation of cerebral functional regions after electroacupuncture (EA) at Yintang (EX-HN3) and GV20 by functional MRI (fMRI). Design A total of 12 healthy volunteers were stimulated by EA at Yintang and GV20 for 30 min. Resting-state fMRI scans were performed before EA, and at 5 and 15 min after needle removal. Statistical parametric mapping was used to preprocess initial data, and regional homogeneity (ReHo) and amplitude of low-frequency fluctuation (ALFF) were analysed. Results ReHo at 5 min post stimulation showed increases in the left temporal lobe and cerebellum and decreases in the left parietal lobe, occipital lobe and right precuneus. At 15 min post stimulation, ReHo showed increases in the left fusiform gyrus; lingual gyrus; middle temporal gyrus; postcentral gyrus; limbic lobe; cingulate gyrus; paracentral lobule; cerebellum, posterior lobe, declive; right cuneus and cerebellum, anterior lobe, culmen. It also showed decreases in the left frontal lobe, parietal lobe, right temporal lobe, frontal lobe, parietal lobe and right cingulate gyrus. ALFF at 5 min post stimulation showed increases in the right temporal lobe, but decreases in the right limbic lobe and posterior cingulate gyrus. At 15 min post stimulation ALFF showed increases in the left frontal lobe, parietal lobe, occipital lobe, right temporal lobe, parietal lobe, occipital lobe and cerebellum, but decreases in the left frontal lobe, anterior cingulate gyrus, right frontal lobe and posterior cingulate gyrus. Conclusions After EA stimulation at Yintang and GV20, which are associated with psychiatric disorder treatments, changes were localised in the frontal lobe, cingulate gyrus and cerebellum. Changes were higher in number and intensity at 15 min than at 5 min after needle removal, demonstrating lasting and strong after-effects of EA on cerebral functional regions.