Multiple sclerosis (MS) is a chronic neurological disease involving inflammation. Brain hypoxia, or low brain oxygenation, in MS is an emerging field of study. It has been shown that some MS patients have reduced cerebral blood flow (CBF), but the mechanism is unclear. Experimental autoimmune encephalomyelitis (EAE) is a mouse model used to study inflammation-associated neurodegeneration. Using perfusion MRI and immunohistochemistry, we demonstrated that CBF reduction in EAE may be due to cerebral blood vessel occlusion in response to systemic inflammation. CBF reduction, coupled with brain inflammation, is a likely cause of hypoxia in MS.