Atopic dermatitis (AD) is a T helper (Th) 2 cell-mediated allergic disease, which features increased number of immunocytes and level of Th2-associated cytokines. Fucoidan is well known a naturally occurring agent effectively ameliorating many AD symptoms. Though these alleviative effects are exhilarating, the mechanisms behind, however, are still rather limited. In this study, we report that fucoidan derived from Cladosiphon okamuranus (FT) inhibits nitric oxide (NO) production by exerting its anti-inflammatory ability. Topical application on animals show that FT promotes skin repair, reduces immunocyte proliferation, and decreases serum IgE level. In histological analysis, FT favorably reduces epidermal hyperplasia and eosinophilic infiltration. The pharmacodynamics mechanism of FT is determined by means of down-regulating AD-associated cytokines (IL-4, IL-5, IL-22, IL-33, and TSLP) and up-regulating TGF-β1 level. Moreover, FT can regulate systemic immunity by enhancing tolerogenic dendritic cells (Tol-DCs) to activate regulatory T cells (Treg) differentiation and to decrease the population of Th22 and memory B cells. Overall, topical application of FT is able to enhance Treg secreting TGF-β1 and to down-regulate Th2 cell-mediated immunity so that AD symptoms are significantly alleviated. Thereby, FT is an ideal drug candidate potentially replacing or complementing corticosteroids to be developed and used as a therapeutic agent to treat AD.