Atopic dermatitis (AD) is a chronic inflammatory skin disease that is associated with intestinal microflora. Since specific probiotics may have better efficacy for AD, we determined the efficacy of Pediococcus acidilactici SRCM102024 (PA) for treating AD in HaCaT cells and NC/Nga mice and explored the mechanism of action. AD-like pathology was induced in HaCaT cells and the dorsal skin of Nc/Nga mice by local exposure to 2,4-dinitrochlorobenzene (DNCB). In AD-lesion induced mice, PA in low-, medium- and high-dosages (5 × 10E6, 5 × 10E7 and 5 × 10E8 CFU/kg bw, respectively) and dexamethasone (3 mg/kg bw, positive-control) were orally administered for 5 weeks. The clinical AD severity, serum immunoglobulin E (IgE) and TNF-α, gene expressions of interleukin (IL)-4, IL-13, and TNF-α and gut microflora were measured. PA treatment (100–300 CFU/mL) dose-dependently increased cell survival in DNCB-induced HACAT cells. PA reduced the relative mRNA expression of PAR-2, TNF-α, IL-4 and IL-13 in the cells. In dorsal skin of Nc/Nga mice applied with DNCB, PA dose-dependently attenuated erythema, hemorrhage, edema, excoriation, dryness and scratching behavior and PA-H improved the clinical symptoms similar to the positive-control. PA-M and PA-H treatment significantly prevented the disturbance of the dorsal skin tissues and decreased the inflammatory cellular infiltrate of mast cells, compared to the control. PA dose-dependently reduced serum IgE and TNF-α concentrations and the mRNA expression of TNF-α, IL-4, and IL-13 in dorsal skin. In gut microflora, relative counts of Lactobacillales, Butyricicoccus and Ruminococcus were decreased in the AD-control compared to the positive-control and the PA-M and PA-H prevented their decrease. However, the positive-control increased serum AST and ALT activities, indicating liver damage as an adverse effect. In conclusion, oral treatment of PA (human equivalent 1 × 10E9-1 × 10E10) relieved the AD symptoms by dose-dependently preventing over-activation of the immune response. Oral PA intake may be a safe and effective alternative therapy for AD.