Lithospermum erythrorhizon Sieb. et Zucc. (LE) is widely used in the treatment of abnormal skin conditions, but its systemic efficacy, especially in atopic dermatitis (AD), is not clear. To examine the systemic efficacy of LE on the clinical manifestation of AD-like skin lesions, NC/Nga mice, a murine model of AD, were fed a control diet (group CA: atopic control) or a diet with a 70% ethanol extract from 5% LE (group LE) for 10 weeks. In group LE, the clinical manifestation of AD-like skin lesions was prevented as the level of serum IgE, epidermal hyperproliferation, and the number and duration of scratching episodes, which were greater in group CA, were significantly reduced to a similar level of the normal control group of BALB/c mice (group C). In addition, the level of ceramides, the major lipid maintaining the epidermal barrier, in the epidermis of group LE was increased, and was inversely associated with a decreased protein level of ceramidase, an enzyme of ceramide degradation. However, the mRNA and the protein levels of serine palmitoyl transferase (enzyme for de novo ceramide synthesis) in groups C, CA and LE did not differ. It was demonstrated that oral supplementation with LE extract prevented the development of atopic dermatitis with reducing ceramide degradation coupled with a low expression of ceramidase protein.