Abstract UDP-α-D-galactofuranose: β-galactofuranoside β-(1→5)-galactofuranosyltransferase, known as GfsA, is essential in synthesizing β-(1→5)-galactofuranosyl oligosaccharides that are incorporated into the cell wall of pathogenic fungi. This study analyzed the structure and function of GfsA from Aspergillus fumigatus. To provide crucial insights into the catalytic mechanism and substrate recognition, the complex structure was elucidated with manganese (Mn2+), a donor substrate product (UDP), and an acceptor sugar molecule (β-galactofuranose). In addition to the typical GT-A fold domain, GfsA has a unique domain formed by the N- and C-termini. The former interacts with the GT-A of another GfsA, forming a dimer. The active center that contains Mn2+, UDP, and galactofuranose forms a groove structure that is highly conserved in the GfsA of Pezizomycotina fungi. Enzymatic assays using site-directed mutants were conducted to determine the roles of specific active site residues in the enzymatic activity of GfsA. The predicted enzyme–substrate complex model containing UDP-α-D-galactofuranose characterized a specific β-galactofuranosyltransfer mechanism to the 5ʹ-OH of β-galactofuranose. Overall, the structure of GfsA in pathogenic fungi provide insights into the complex glycan biosynthetic processes of fungal pathogenesis and may inform the development of novel antifungal therapies.