This study attempted to find an efficient method for the preparation of high-purity galactooligosaccharides (HP-GOS) using β-galactosidase and yeast fermentation. GOS prepared using Lactozym 3000L showed the greatest enhancement in total GOS of the six β-galatosidases tested. GOS alone achieved 51% conversion of initial lactose. GOS production was enhanced by fermentation with commercial yeast (Saccharomyces cerevisiae); its concentration reached 71% after 36h fermentation with 8% yeast. Component sugar analysis with HPLC indicated that HP-GOS fermented with S. cerevisiae showed significantly increased levels of 4’/6’-galactosyllactose and total GOS as well as a significantly decreased glucose level. HP-GOS facilitated the growth of Lactobacillus sp. (L. acidophilus and L. casei) and Bifidobacterium sp. (B. longum and B. bifidum). In sum, high-purity GOS has been successfully produced through both an enzymatic process and yeast fermentation. GOS encourages the growth of bacteria such as Lactobacillus and Bifidobacterium that may be beneficial to human gastrointestinal health.