Inulin has been widely used as a cheap material to produce many valuable products such as inulooligosaccharides. In this study, an inulooligosaccharide-producing endoinulinase was identified from Aspergillus arachidicola. The gene encoding the mature endoinulinase was cloned and intracellularly overexpressed in Escherichia coli. The recombinant endoinulinase was purified by nickel affinity chromatography. The optimum pH and temperature were pH 5.5 and 60 °C, respectively. It was highly thermostable at up to 55 °C for 2 h, however easily inactivated at higher temperatures. The enzyme efficiently produced inulooligosaccharides from inulin, with inulotriose and inulotetraose as major products. When 10, 30, 50, and 100 g L of inulin was used as substrate, the final conversion ratio of total inulooligosaccharides reached 88.4%, 83.5%, 80.2%, and 60.1%, respectively. In addition, yeast treatment was first developed to improve the inulooligosaccharides purity by specifically consuming sucrose and monosaccharides without any losses in inulooligosaccharides content.