Atopic dermatitis (AD) leads to skin barrier abnormalities and immune dysfunction. As the topical steroids commonly used to treat AD have side effects from long-term use, research into safer treatments for AD is greatly needed. The medicinal herb Gardenia jasminoides improves AD symptoms via skin barrier activation and T helper 2-mediated immune response regulation. Crocin, a bioactive component within the extract, is dispensible for its restorative effects. As such, this work explored the effects of Gardenia jasminoides extract without crocin (GjexCr) on AD symptoms in a DfE-induced AD model in 6-week-old male NC/Nga mice (25.0 ± 0.25 g, n = 10 each, 6 groups). Using histological and behavioral assays, the effects of GjexCr on dermatitis scores, scratching behavior, skin barrier activation, and serum levels of IgE, chemokines, and cytokines were analyzed. In addition, the major components from the GjexCr extract were analyzed by high-performance liquid chromatography and validated in the AD model. GjexCr reduced ear thickness due to hyperkeratosis, dermal thickening, and scratching behavior and restored dermatitis scores in AD-induced mice. GjexCr administration also decreased inflammation and mast cell infiltration, as well as modulated skin barrier recovery by upregulating the production of epidermal proteins. Moreover, GjexCr administration attenuated imbalanced immune responses. Furthermore, geniposide, the main component of GjexCr, improved AD symptoms in DfE-treated NC/Nga mice. Thus, GjexCr could be a suitable treatment for protecting the skin barrier in AD-like skin lesions and a potential therapy for AD.