Background and PurposeBlood‐brain barrier (BBB) breakdown is one of the most crucial pathological changes of cerebral ischemia‐reperfusion (I/R) injury. Trilobatin (TLB), a naturally occurring food additive, exerts neuroprotective effect against cerebral I/R injury as demonstrated in our previous study. This study was designed to investigate the effect of TLB on BBB disruption after cerebral I/R injury.Experimental ApproachRats with focal cerebral ischemia caused by transient middle cerebral artery occlusion (MCAO) and brain microvascular endothelial cells along with human astrocytes to mimic BBB injury caused by oxygen and glucose deprivation (OGD)/reoxygenation (OGD/R).Key resultsThe results showed that TLB effectively maintained BBB integrity and inhibited neuronal loss following cerebral I/R challenge. Furthermore, TLB increased tight junction proteins including ZO‐1, Occludin and Claudin 5, decreased the levels of apolipoprotein E (APOE) 4, cyclophilin A (CypA), and phosphorylated nuclear factor kappa B (NF‐κB), thereby reduced proinflammatory cytokines. Additionally, TLB also decreased Bax/Bcl‐2 ratio and cleaved‐caspase 3 level along with reduced the number of apoptotic neurons. Intriguingly, molecular docking and transcriptomics predicted MMP9 was a prominent gene evoked by TLB treatment. Furthermore, the protective effect of TLB on cerebral I/R‐induced BBB breakdown was largely abolished by overexpression of MMP9, and the beneficial effect of TLB on OGD/R‐induced the loss of BBB integrity in human brain microvascular endothelial cell and astrocyte co‐cultures was markedly reinforced by knockdown of MMP9.Conclusions and implicationsOur findings reveal a novel property of TLB: saving BBB disruption following cerebral I/R via targeting MMP9 and inhibiting APOE4/CypA/NF‐κB axis.