Purpose: Azelaic acid is a natural keratolytic, comedolytic, and antibacterial drug that is used to treat acne. The topical application of azelaic acid is associated with problems such as irritation and low permeability. For dissolving, the problem is that microemulsion (ME) is used as a drug carrier. The aim of this study was to increase the azelaic acid affinity in the follicular pathway through ME. Methods: Azelaic acid-loaded MEs were prepared by the water titration method. The properties of the MEs included formulation stability, particle size, drug release profile, thermal behavior of MEs, the diffusion coefficient of the MEs and skin permeability in the non-hairy ear skin and hairy abdominal skin of guinea pig were studied in situ. Results: The MEs demonstrated a mean droplet size between 5 to 150 nm. In the higher ratios of surfactant/co-surfactant, a more extensive ME zone was found. All MEs increased the azelaic acid flux through both hairy and non-hairy skin compared with an aqueous solution of azelaic acid as a control. This effect of the ME was mainly dependent on the droplet diffusion coefficient and hydrodynamic radius. MEs with a higher diffusion coefficient demonstrated higher azelaic acid flux through hairy and non-hairy skin. Drug flux through both skins was affected by the surfactant/co-surfactant ratio in that the higher ratio increased the azelaic acid affinity into the follicular pathway. Conclusion: Finally, the ME with the highest droplet diffusion coefficient and the lowest surfactant/co-surfactant ratio was the best ME for azelaic acid delivery into the follicular pathway.