Ischemic stroke remains one of the leading causes of death and long-term disability in humans. As an important barrier between the brain and the periphery, the blood-brain barrier (BBB) plays an important role in maintaining environmental homeostasis. The interaction between endothelial cells, a major component of the BBB, and other cells in the neurovascular unit is particularly critical. After ischemic stroke, BBB leakage and endothelial cell dysfunction lead to extravasation of plasma components and infiltration of circulating inflammatory cells, further activating microglia and aggravating lesion injury. This article will review the pathways and mechanisms of endothelial cells on microglia after ischemic stroke based on the latest research progress.