Structurally well-defined, homogeneous glycopeptides and glycoproteins are indispensable tools for functional glycomics studies. By screening of various endo-β-N-acetylglucosaminidases using an appropriate synthetic donor and acceptor substrates, we have found that the Flavobacterium meningosepticum endo-β-N-acetylglucosaminidases glycosidases (GH family 18), including Endo-F2 and Endo-F3, were able to glycosylate α-1,6-fucosylated GlcNAc derivative to provide natural, core-fucosylated complex type N-glycopeptides. The Endo-F2 and Endo-F3 were efficient for transferring both sialylated and asialylated glycans and were highly specific for an α-1,6-fucosyllated GlcNAc-peptide as acceptor for transglycosylation, as they showed only marginal activity on non-fucosylated GlcNAc-peptide. In contrast, we found that the commonly used endoglycosidases such as Endo-A and Endo-M, which belong to GH family 85, were unable to take α-1,6-fucosyl-GlcNAc derivative as acceptor for transglycosylation. The novel activity of Endo-F2 and Endo-F3 was successfully applied for a highly convergent chemoenzymatic synthesis of a full-size CD52 glycopeptide antigen carrying both terminal sialic acid and core fucose. This is the first report on endoglycosidases that are able to glycosylate α-1,6-fucosylated GlcNAc derivatives to form natural core-fucosylated glycopeptides.