Upon inflammation, leukocytes extravasate through endothelial cells. When they extravasate in a paracellular manner, it is generally accepted that neighbouring endothelial cells physically disconnect to open cell-cell junctions, allowing leukocytes to cross. When carefully examining endothelial junctions, we found a partial membrane overlap of endothelial cells beyond VE-cadherin distribution. These overlaps are regulated by actin polymerization and, although marked by, do not require PECAM-1, nor VE-cadherin. Neutrophils prefer wider membrane overlaps as exit sites. Detailed 3D analysis of endothelial membrane dynamics during paracellular neutrophil transmigration in real-time, at high spatiotemporal resolution using resonant confocal and lattice light-sheet imaging, revealed that overlapping endothelial membranes form a tunnel during neutrophil transmigration. These tunnels are formed by the neutrophil lifting the membrane of the upper endothelial cell while indenting and crawling over the membrane of the underlying endothelial cell. Our work shows that endothelial cells do not simply retract upon passage of neutrophils but provide membrane tunnels, allowing neutrophils to extravasate. This discovery defines the 3D multicellular architecture in which the paracellular transmigration of neutrophils occurs.