Transcytosis, a widely described process concerning transport of macromolecules between the apical and basolateral sides in various cell types, is extremely important for multicellular organisms to selectively exchange materials in different microenvironments while maintaining cellular and body homeostasis. Uncontrolled transcytosis is involved in a wide range of pathophysiological processes. Lipid rafts (LRs), the sphingolipid and cholesterol-enriched membrane microdomains, enable to form different functional membrane macrodomains or platforms upon stimulations. In particular, ceramide-enriched membrane microdomains play extremely critical roles in LRs clustering or platform formations. Notably, various transcytosis-related molecules are tightly correlated with LRs and ceramide. We attempt to summarize the basic and advanced information about the roles of different types of transcytosis in human health and diseases, and the types and functions of LRs involved in transcytosis, as well as multiple transcytosis-related molecules associated with LRs and ceramide. It is hoped that all information and discussions could provide much more comprehensive insights into the understanding of the association of LRs with transcytosis, as well as shed some new light on the translational significance in this area.