Background: Atopic dermatitis (AD) is known to be affected by neuropeptides. However, the mechanism underlying this phenomenon is unclear. This study analyzed the mechanism(s) responsible for the influence of β-endorphin (β-End) or N-acetyl-β-endorphin (acetyl-β-End) on AD. Methods: Specific pathogen-free (SPF) and conventional NC/Nga mice were used for the studies. Conventional (not SPF) mice, spontaneously develop dermal symptoms similar to that of patients with AD. In the present study we treated mice with 5 µg/mouse of β-End or acetyl-β-End for 20 days. In addition, a histone acetyltransferase inhibitor II (HAT inhibitor, 100 mg/kg) was given for 20 days to examine its effects on the acetylation of the β-End. Results: The symptoms of the conventional group were ameliorated by both β-End and acetyl-β-End treatment, although acetyl-β-End treatment more effectively relieved the symptoms than β-End, and the improvement induced by the β-End treatment disappeared following HAT inhibitor treatment. Conclusions: These observations suggested that β-End or acetyl-β-End treatment can suppress the symptoms of AD in the mice, and that the effect of the β-End is induced by the acetylation of the β-End by HAT.