Neuroprotective therapies have made little progress in the recent past. Vascular components of injury contributing to the development and progression of neuronal injury, the inability of drugs to pass the blood-brain barrier (BBB) and unsuitable animal models used for mimicking stroke pathophysiology have been recognized as major factors responsible of treatment failure. The molecular mechanisms underlying disturbances of BBB function after stroke are poorly understood. Microvascular cells are polarized cells forming a tight barrier, which is complemented by membrane-bound ATP-binding cassette (ABC) transporters both on the luminal and abluminal endothelial membrane, giving rise to two key features, BBB tightness and polarity. Both BBB tightness and polarity are dysregulated upon stroke. Our study was carried out to study the underlying molecular mechanisms regulating BBB integrity and polarity. As such, the relevance of liver X receptor (LXR), the role of the apolipoprotein ApoE and effects of hypercholesterolemia, a highly prevalent risk factor for vascular diseases were investigated. By means of pharmacological studies using a LXR agonist, T0901317, using Western blots analysis, protein interaction studies and pull-down assays, we showed that LXR activation preserved BBB integrity and decreased BBB leakage after focal cerebral ischemia induced by middle cerebral artery (MCA) occlusion, representing a promising strategy to prevent post-ischemic brain swelling, a frequent complication of ischemic stroke. On the molecular level, the anti-edematous effect was caused by deactivation of microvascular calpain-1/2 and MMP-2/9 protease activity, resulting in the stabilization of p120 catenin, thereby decreasing RhoA and increasing Cdc42 activity, thus modulating the expression, phosphorylation and assembly of tight junction (TJ) proteins. BBB enhanced integrity did not influence BBB polarity, as upon LXR activation the expression of the ABC transporters ABCB1, ABCC1, ABCA1 and ABCG1 expression was similarly increased. By means of genetic knockout, protein delivery and pharmacological signal transduction inhibition experiments, we demonstrated that ApoE controls the polarized expression changes of ABC transporters following stroke, presumably via its receptor ApoER2, which is mainly expressed at the abluminal side of brain capillaries and acts as sensor of BBB leakage. As such, ApoE binding to ApoER2 deactivates Jun-Kinase-1/2 (JNK-1/2) and c-Jun, thus transcriptionally increasing luminal endothelial ABCB1 and decreasing abluminal ABCC1 expression, thereby reducing the accumulation of the pharmacological model compound FK506 in the ischemic brain. Interestingly, BBB tightness, as evaluated by measuring by serum IgG extravasation, was not influenced by ApoE deficiency. Based on our data, ApoE regulates an endogenous cellular response, which prevents the accumulation of potentially toxic blood-derived molecules in the ischemic brain, but also impedes brain pharmacotherapies. Deactivation of ApoER2, based on our data may represent a promising strategy to ameliorate drug delivery to the stroke brain. Hypercholesterolemia is a major risk factor of ischemic stroke. By means of Western blots, protein-protein interaction and pull-down assays, we showed that hypercholesterolemia increases BBB leakage upon stroke without influencing ABC drug transporters. This increased permeability was accompanied by and exacerbated activation of calpain-1/2, MMP-2/9 and downregulation of TJ proteins under hypercholesterolemic conditions. The effect of hypercholesterolemia on BBB permeability was associated with the overexpression of the angiotensin II type 1 receptor (AT1R), with overactivation of its downstream target RhoA and RhoA’s activator, the leukemia associated Rho GEF (LARG). Our results show that BBB tightness and polarity are regulated by separate mechanisms. Our results offer new perspectives for the treatment of cerebrovascular diseases. As such, LXR agonists might be used for the treatment of brain edema, ApoE regulation or ApoER2 blockade might be a novel strategy to enhance neuroprotective drug entry. The effects of hypercholesterolemia on BBB integrity should be taken more thoroughly in account in translational stroke studies.