Allergic conjunctivitis (AC) is an inflammatory disease of the conjunctiva, which is characterized by antigen challenge and toll-like receptor 2 (TLR2) activation. Here, a designed small peptide ZY12 was found to contain therapeutic potential in staphylococcal enterotoxin B (SEB)-induced AC model. ZY12 treatment showed the remission of clinical signs, plasma total IgE levels, number of mast cells and the proportion of degranulated mast cell in AC mice. Levels of Th2 cytokines (IL-4, IL-5, IL-13) in the lymph nodes or spleen were significantly decreased while those of Th1 cytokine (IFN-γ) were increased in ZY12 treated group, suggesting a protective role of ZY12 in AC by mediating the balance of Th1/Th2 cytokines. Importantly, ZY12 significantly inhibited TLR2 expression in conjunctival tissue. Combined its therapeutic effects with TLR2 inhibitory function, ZY12 might be an ideal candidate for the development of new therapeutic agent for allergic disease.