FOXF2, a major risk gene for stroke and SVD, the mechanisms of which are insufficiently understood. CRISPR/Cas9-mediated knockout of FOXF2 induced key features of BBB dysfunction, including compromised cell junction integrity, decreased transendothelial electrical resistance and dysregulated caveolae formation. Proteomic analysis of human iPSC derived endothelial cells revealed an impairment of pathways related to endocytosis and cell junctions, confirming a role of FOXF2 in BBB function. The observed disease features phenocopy those seen in an endothelial cell-specific mouse model of Foxf2 deficiency that we have developed in parallel, validating the relevance of our human BBB model to investigate neurovascular disorders.