The mechanisms underlying neurodegeneration in multiple sclerosis (MS) remain incompletely understood. In this study, we aimed to investigate the role of vascular dysfunction in cortical neurodegeneration using a chronic cranial window model of experimental autoimmune encephalomyelitis (EAE) in mice.Following the establishment of chronic cranial window and induction of EAE with MOG peptides in C57BL6/J mice, we assessed cerebrovascular reactivity (CVR) using both laser speckle contrast imaging (LSCI) and optical signal imaging (IOSI) in awake animals, with stimuli including air puff to the whisker pad and 5% hypercapnia. Histological analysis was performed using immunofluorescence and confocal imaging.We observed a significant reduction in cortical CVR during peak inflammation in the EAE group, as detected by LSCI after 5% hypercapnia (p=0.008) and IOSI after whisker pad stimulation. Additionally, there was a significant increase in CD13+ pericyte coverage (p=0.001), focal IgG deposition within the microvascular lumen (p=0.04), and microglial activation in the cortex of EAE mice (p=0.04). Foci exhibiting loss of NeuN reactivity were also detected in subpial and intracortical regions in EAE, but not in control mice (p=0.03). Axonal loss, revealed by SMI-32 staining, was also evident (p=0.007). Furthermore, we observed an increased amount of CD45+ leukocytes stalled in microvessels (p=0.03) in EAE. Microglial activation was particularly evident around affected microvessels, even in regions without detectable leukocytic infiltration.Our findings clearly demonstrate that soluble factors in EAE lead to cortical microvascular dysfunction by affecting elements of the neurovascular unit and causing leukocyte stalling in capillaries, ultimately resulting in neurodegeneration.