Blood brain barrier (BBB) hyperpermeability and brain edema contribute to increased seizure susceptibility and brain injury in status epilepticus (SE). The endothelial glycocalyx is the coating on luminal side of the endothelium and can be considered as the first barrier of BBB. Currently, little is known about the effects of endothelial glycocalyx in SE. We hypothesized glycocalyx degradation could be considered as a first step in the pathophysiology of SE. The study aimed to investigate the impacts of glycocalyx integrity loss on brain damage in a C57BL/6 mouse model of SE induced by lithium-pilocarpine and whether heparin, a competitive antagonist against heparinase, improves survival and neurological outcome. Compared to controls, glycocalyx was significantly degraded after SE, which was mitigated by heparin. The glycocalyx disruption was associated with higher BBB permeability and aggravated brain edema at 72 h after SE, as well as lower survival rate and poorer neurologic outcome. Conversely, preservation of glycocalyx by heparin could reduce SE-induced activation of glia cells, BBB leakage, brain edema, decrease the expressions of inflammatory factors and improve neurologic outcome. The study highlights the importance of glycocalyx degradation in cerebral edema and SE outcome, and indicates heparin treatment may be a new strategy for brain protection in SE.