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The growing global market of dairy products has led to the need for alternative approaches regarding whey valorization, which is the primary by-product of cheese and strained yogurt production. In this context, prebiotic galactooligosaccharides can be produced enzymatically from whey using commercially available β-galactosidases. A comparative study was conducted to assess the production of galactooligosaccharides from sweet and acid whey, thereby employing two commercial β-galactosidases from <i>Aspergillus oryzae</i> and <i>Kluyveromyces lactis</i>. The study considered the initial lactose content and enzyme load as variables. The maximum yields of galactooligosaccharides in concentrated sweet whey (15% <i>w</i>/<i>v</i> initial lactose) and raw acid whey (3.1% <i>w</i>/<i>v</i> initial lactose) reached 34.4 and 14.7% with lactase from <i>Kluyveromyces lactis</i> (0.13 U/mL), respectively. The corresponding galactooligosaccharide yields for lactase from <i>Aspergillus oryzae</i> were equal to 27.4 and 24.8% in the most concentrated sweet and acid whey, respectively, using enzyme loads of 2 U/mL in sweet whey and 1 U/mL in acid whey. Concerning the profile of the produced galactooligosaccharides, the <i>Kluyveromyces lactis</i> lactase hydrolyzed lactose more rapidly and resulted in higher levels of allolactose and lower levels of 6-galactosyl-lactose, compared to the lactase from <i>Aspergillus oryzae</i>, and achieved in both cases a polymerization degree of up to six.