Hyperlipidemia, one of the cardiovascular (CV) risk factors, is associated with an increase in the risk for dementia. Repetitive transcranial magnetic stimulation (rTMS) was applied over the right dorsolateral prefrontal cortex (DLPFC) to modulate serum lipid levels in older adults. Participants received 10 sessions of rTMS or sham stimulation intervention within 2 weeks. The serum lipid and thyroid hormone-related endocrine levels were assessed before and after the treatment. We found that rTMS significantly decreased serum lipid levels, including the total cholesterol (CHO) and triglyceride (TG); meanwhile, it also increased the thyroid-stimulating hormone (TSH) as well as thyroxine (T4) levels. This suggests that rTMS modulated the serum lipid metabolism by altering activity in the hypothalamo-pituitary-thyroid (HPT) axis. The trial was registered on the website of Chinese Clinical Trial Registry (http://www.chictr.org.cn).