To investigate the effects of scalp electroacupuncture on the expression of NF-κB p65 and COX-2 protein in the hippocampus and hypothalamus of rats with chronic fatigue syndrome (CFS). Methods: Thirty-six pathogen-free male SD rats were randomly divided into the normal group, model group, and treatment group with 12 rats per group. The CFS animal model was established. The treatment group was given acupuncture therapy to the Baihui, emotional zone 1, and sensory zone. Immunohistochemistry was employed to examine the variation in expression of NF-κB p65 and COX-2 in the hippocampus and of rats in each group. Results: Compared with that of the normal group, the hippocampus and hypothalamus of rats in the model group showed significantly increased positive expression of NF-κB p65 and COX-2 protein (P< 0.01). Compared with that of the model group, the hippocampus and hypothalamus of rats in the treatment group displayed significantly reduced expression of NF-κB p65 positive cells (P<0.01). Conclusion: Acupuncture can reduce the expression of NF-κB p65 and COX-2 protein in the hippocampus and hypothalamus of CFS rats.