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UVB rays cause sunburn to lead to various skin damages, despite their necessity for vitamin D synthesis. The outermost layer of the epidermis is the cornified envelope (CE), characterized by a lipid-protein cross-linked complex structure. UVB radiation disrupted the CE structure, leading to skin barrier dysfunction and a decrease in epidermal moisture. Phycocyanin (PC) and its enzyme-digested product (EDPC) showed repair-enhancing action by their oral post-administration subsequent to UVB pre-radiation in hairless mice. The repair-promoting effect resulted from transcriptional events mediated by their administrations. DNA microarray analyses revealed a unique molecular mechanism underlying this effect. Several genes, including Lce, Sprr, Krt, Csta, and Degs, that encoded CE components of proteins, protease inhibitors, and/or enzymes, exhibited reasonable upregulation or downregulation in expression. Post-administration following UVB pre-radiation caused additionally/amelioratively up- or down-regulated expression of these genes.These findings indicate that PC, especially EDPC, had the repair-enhancing effect on UVB-induced skin barrier dysfunction when applied post-UVB exposure.