Abstract The synthesis of 6-selenophenyl derivatives of β-1,3 and β-1,4 disaccharides has been explored for the purpose of extending our epoxide fluoridolysis methodology to the synthesis of 5-fluoro analogues of N-acetyl isolactosamine (isoLacNAc, lacto- N-biose) and N-acetyl lactosamine (LacNAc) glycosides. Successful synthesis of the C-6 selenium-containing disaccharides was achieved via Lewis acid-mediated donor and acceptor substrates, the latter containing a selectively protected C-6 hydroxyl group for ultimate conversion to the desired 6-selenophenyl disaccharides. In contrast, the use of selenium-containing acceptor substrates under a variety of conditions failed to yield the desired selenium-containing disaccharides. Oxidation of the 6-selenophenyl derivatives to the corresponding selenoxides followed by thermal elimination yielded the exocyclic olefins, which were converted to the 5,6-epoxides. Epoxide fluoridolysis yielded the desired target compounds, 5-fluoro β-octyl glycoside analogues of type 1 and type 2 glycans. The newly synthesized fluorine-containing disaccharides have potential application as fucosyltransferase substrates, both for mechanistic studies and in the chemoenzymatic synthesis of fluorine-containing oligosaccharides.