Brain hypoxia is present in multiple sclerosis, a condition associated with inflammation. Hypoxia may be related to inflammation. Quantitative susceptibility mapping (QSM) is sensitive to deoxyhemoglobin and so hypoxia. Here, we combined perfusion MRI with QSM to assess hypoxia and cerebral blood flow (CBF) in the lipopolysaccharide (LPS) inflammatory model. We report a reduction in susceptibility, as well as a significant reduction in CBF, in the cortex of the LPS model. As reduced tissue susceptibility was observed in more hypoxic subjects, this could be consistent with hypoxia in the inflammatory model, and QSM might be a possible biomarker.