Increases in adsorptive mediated transcytosis (AMT) at the blood-brain barrier (BBB) are linked to many brain disorders. In a healthy brain, AMT is suppressed by sphingosine-1-phosphate (S1P) receptor 1 (S1PR1) signaling. Low levels of S1P lead to a rise in AMT, but the mechanisms are incompletely understood. Here, we explored whether the rises in AMT are caused by the loss of the endothelial glycocalyx (gcx). We used two-photon microscopy in mice with low S1P plasma levels (Apom-/-) and developed a novel photobleaching approach to measure gcx in vivo at distinct classes of cerebral microvessels, i.e., arterioles, capillaries, and venules. We show that S1P signaling impairment reduced gcx in arterioles but not in other vessel segments. The location of gcx loss corresponded to the vascular topology of AMT increases. The S1PR1 agonist SEW2871 restores low levels of AMT in Apom-/- mice but did not restore the gcx within the same time window. We propose that while the gcx loss may contribute to AMT increase, restoring gcx is not necessary for AMT to return to normal. These data establish a new imaging method to study gcx in the living mouse brain, demonstrate zonation of gcx in cerebral microvessels, and suggest differences in vascular susceptibility to gcx loss in disease states.