Medicinal herbs produce valuable substances with therapeutic potential. The chemical structures of those substances are often converted by gut microbiota. Our previous studies showed that several kinds of bioactive molecules are newly generated in fermented medicinal herbal extract with plant-derived lactic acid bacteria (LABs). The fermented extract of Atractylodes Japonica Rhizoma (AJR), which is designated as "Byakujutsu" in Japan, with a plant-derived LAB strain IJH-SONE68 was prepared and whether the fermented extract could help reduce symptoms of food allergies, especially wheat intolerance, was confirmed using animal model. It has been found that the fermented extract significantly ameliorates the anaphylaxis score (from 3.0 to 1.0, = 0.003) of gliadin-induced allergic model mice (specific-pathogen-free, BALB/cJ) accompanied with the modulation of serum total immunoglobulin E (IgE) (from 778 to 518 ng/mL, = 0.006), interferon (IFN)-γ (from 6.6 to 9.5 pg/mL, < 0.001), and interleukin (IL)-4 (from 32.0 to 9.1 pg/mL, < 0.001) levels. The fermented AJR extract may modulate the Th1/Th2 cell balance to alleviate the symptoms of gliadin-induced anaphylaxis in mice. The present study supports the view that the fermentation of medicinal herbal extract prepared using LABs may be a useful procedure for producing therapeutic potential compounds to maintain health.