Carotid endarterectomy (CEA) as a procedure has been shown effective in reducing the risk of stroke for patients with severe stenosis. The impact of CEA on the functional connectivity of the brain has not been assessed to this point. Nine patients underwent resting state fMRI pre-operatively and 1 month and 6 months post-operatively. Analysis was performed using seed based analysis and matrix based analysis to determine if there were functional connectivity changes as a result of CEA. Seed based and matrix based analysis showed that there were significant functional connectivity changes as result of CEA.