The enzyme fructosyltransferase (FTase) is responsible for the sucrose hydrolysis followed by the transfer of fructose oligomers in the formation of fructooligosaccharides (FOS). FOS are included in the prebiotic group, are low in calories, are non-cariogenic and stimulate the growth of desirable bacteria present in the intestinal microbiota consequently decreasing the pathogenic microorganisms present in the intestine and facilitating calcium and magnesium adsorption. Fructooligosaccharides are also used in animal nutrition. But the discovery of more efficient enzymes with high activity and stability is still necessary, and this is a fact that still arouses the interest of researchers. FTase is found in different sources such as microorganisms and plants; however, filamentous fungi have been gaining ground in the industry for being excellent enzyme producers, especially the genus Aspergillus. This brief review highlights the different sources of fructosyltransferase, its biochemical characteristics, its performance in different bioprocesses and its industrial applications.