Escherichia coli K1 has been shown to invade human brain microvascular endothelial cells (HBMEC) in vitro and translocate the blood-brain barrier in vivo, but it is unclear how E. coli K1 traverses HBMEC. We have previously shown that internalized E. coli K1 is localized within membrane-bound vacuole in HBMEC. The present study was carried out to understand intracellular trafficking of E. coli K1 containing vacuoles (ECVs) in HBMEC. ECVs initially acquired two early endosomal marker proteins, EEA1 and transferrin receptor. Rab7 and Lamp-1, markers for late endosome and late endosome/lysosome, respectively, were subsequently recruited on the ECVs, which was confirmed with flow cytometry analysis of ECVs. However, ECVs did not obtain cathepsin D, a lysosomal enzyme, even after 120 min incubation, suggesting that E. coli K1 avoids lysosomal fusion. In contrast, isogenic K1 capsule-deletion mutant obtained early and late endosomal markers on vacuolar membranes and allowed lysosomal fusion with subsequent degradation inside vacuoles. This observation was consistent with the decreased intracellular survival of K1 capsule-deletion mutant, even though the binding and internalization rates of the mutant were higher than those of the parent E. coli K1 strain. This is the first demonstration that E. coli K1, via the K1 capsule on the bacterial surface, modulates the maturation process of ECVs and prevents fusion with lysosomes, which is an event necessary for traversal of the blood-brain barrier as live bacteria.