Atopic dermatitis (AD) is a chronic inflammatory skin disease. Juniperus Chinensis heartwood has been known to have an excellent antibacterial and anti-inflammatory effect. This study examined the potential of the methanol extract of the Juniperus Chinensis heartwood as a natural dye with an efficacy for the treatment of atopic dermatitis. In an attempt to examine the effect of the Juniperus Chinensis heartwood extract, a skin lesion such as that of AD was induced in the NC/Nga AD mice model by topical administration. DNCB (2.4-dinitrochlorobenzene) was used to induce such AD-like skin lesions. The efficacy of the Juniperus Chinensis heartwood extract in the NC/Nga mice model was assessed by severity of skin lesion (NC mouse score), change in organ weight, serum IgE level, change in epidermal thickness, and mast cell count. The Juniperus Chinensis heartwood extract improved such skin lesions in these NC/Nga mice, and decreased spleen weight and serum IgE level. The results of histopathologic examination revealed that the treatment with the Juniperus Chinensis heartwood extract decreased epidermal thickness and mast cell count. In conclusion, the suppressive effect of local administration of the Juniperus Chinensis heartwood extract verified its potential for application as a natural dye with an efficacy of treatment for atopic dermatitis.