Cow's milk is one of the most common allergenic foods. Cow's milk allergy is mainly an IgE-mediated hypersensitivity reaction, and the major allergens from cow's milk have been found to be caseins, -lactoglobulin, and -lactalbumin. Several peptides derived from bovine casein are known allergens in cow's milk. To reduce their allergenicity, these proteins can be degraded by food-grade peptidases. We succeeded in detection of two peptides, VLPVPQK and FFVAPFPEVFGK, from bovine casein-derived allergen peptides by using an ion trap LC-MS apparatus. This study focuses on the synergistic effects of Streptomyces aminopeptidases belonging to the M1, M24, and M28 families on the degradation of the allergen peptides. From these results, we demonstrated that the combination of M1 and M24 aminopeptidases was the most effective for degrading the abovementioned allergenic peptides.