Ischemic preconditioning (IPC) could protect the blood-brain barrier (BBB), but the underlying mechanism is not well understood. This preclinical study aimed to investigate whether glycocalyx could be involved in the neuroprotective effect of IPC on cerebral ischemia-reperfusion injury (IRI) and the possible mechanism in rat middle cerebral artery occlusion/reperfusion (MCAO/R) model. Neurological deficit scores, infarct volume, and brain edema were measured to assess the neuroprotection of IPC. Several serum biomarkers related to glycocalyx damage, such as hyaluronic acid (HA), heparan sulfate (HS), and syndecan-1 (SYND1), were evaluated, and their changes were normalized to the ratio of postoperative/preoperative concentration. Western blot and immunofluorescence were used to evaluate the content and cellular location of HA-related metabolic enzymes. This study found that (1) IPC improved brain infarction and edema, neurological impairment, and BBB disruption in IRI rats; (2) IPC significantly up-regulated HA ratio and down-regulated HS ratio, but did not affect SYND1 ratio compared with the IRI group. Moreover, the increased HA ratio was negatively related to brain edema and neurological deficit score. (3) IPC affected HA metabolism by up-regulating hyaluronate synthase-1 and matrix metalloproteinase-2, and down-regulating hyaluronidase-1 in brain tissue. Together, this is the first report that the neuroprotective effect of IPC on IRI may be mediated through interfering with glycocalyx in the MCAO/R model.