Cutaneous exposure to food allergens through a disrupted skin barrier is recognized as an important cause of food allergy, and the cutaneous sensitized mouse model has been established to investigate relevant allergic disorders. However, the role of different genetic backgrounds of mice on immune responses to food allergens upon epicutaneous sensitization is largely unknown. In this study, two strains of mice, i.e., the BALB/c and C57BL/6 mice, were epicutaneously sensitized with ovalbumin on atopic dermatitis (AD)-like skin lesions, followed by intragastric challenge to induce IgE-mediated food allergy. Allergic outcomes were measured as clinical signs, specific antibodies and cytokines, and immune cell subpopulations, as well as changes in intestinal barrier function and gut microbiota. Results showed that both strains of mice exhibited typical food-allergic symptoms with a Th2-skewed response. The C57BL/6 mice, rather than the BALB/c mice, were fitter for establishing an epicutaneously sensitized model of food allergy since a stronger Th2-biased response and severer disruptions in the intestinal barrier and gut homeostasis were observed. This study provides knowledge for selecting an appropriate mouse model to study food-allergic responses associated with AD-like skin lesions and highlights the role of genetic variations in the immune mechanism underlying pathogenesis of food allergy.