Acupuncture is widely used to treat various neurodegenerative diseases and can effectively improve cognitive and memory states in Alzheimer’s disease. However, its mechanism is unclear. We speculated that the effect of acupuncture on cognitive function may be associated with reductions in the levels of Aβ and phosphorylated tau in the brain. In this experiment, 60 male Sprague-Dawley rats were randomly divided into control, model, electroacupuncture and nonacupoint groups. We perform electroacupuncture at Shenting (GV24) and bilateral Benshen (GB13) acupoints once a day for 4 weeks in electroacupuncture group (with 1 day of rest after every 6 days of treatment). The electroacupuncture group showed a better performance in cognitive-related behavior tests and significantly lowers the levels of Aβ, p-tau (s396) and p-tau (s404) in the hippocampus. These results may suggest that electroacupuncture at the GV24 and bilateral GB13 acupoints might improve cognitive functions in Alzheimer’s disease by decreasing the levels of Aβ, p-tau (s396) and p-tau (s404) in the brain as these proteins are the main causes of neurological damage and cognitive dysfunction during the pathogenesis underlying Alzheimer’s disease.