AIM: To prepare radix scutellariae microemulsion gel and investigate its therapeutic effect on chronic eczema based on the previous research of radix scutellariae self microemulsion. METHODS: The gel matrix and humectant were optimized by single factor method and response surface method to obtain the formula and preparation technique of the gel. The Franz diffusion cell method was used to evaluate the transdermal properties of microemulsion and microemulsion gel in vitro. By establishing a chronic eczema model in the mouse ear, the swelling degree, swelling inhibition rate, pathological changes and tumor necrosis factor α (TNF-α), Interleukin-1β (IL-1β) and interleukin?6 (IL-6) of radix scutellariae microemulsion gel were measured, to investigate the therapeutic effect on chronic eczema in mice. RESULTS: The physical and chemical properties of radix scutellariae microemulsion gel were stable. Compared with microemulsion, the microemulsion gel had better transdermal performance. The cumulative transdermal amount of baicalein and wogonin, the main components of microemulsion gel, was 1.85 times and 2.77 times of that of microemulsion respectively. Moreover, the steady flow rate and permeability coefficient of microemulsion gel significantly increased, and the lag time significantly shortened. Pharmacodynamic study showed that compared with the model group, the radix scutellariae microemulsion gel could significantly reduce the ear swelling of mice (P<0.05), and the serum inflammatory factor TNF-α, IL-1β and IL-6 reduced content by over 37%. Compared with the radix scutellaria aqueous extract and aqueous extract gel, the treatment of chronic eczema was better. CONCLUSION: The preparation process of radix scutellaria microemulsion gel is feasible, with strong transdermal property, and a significant therapeutic effect on chronic eczema.