Transdermal Drug Delivery System (TDDS) nowadays is one of the most important topics to deliver certain drugs in a safe, efficient and sustained manner and to achieve the acceptance of the patient. Microemulsions (MEs) are known to be good drug delivery systems for transdermal application. The droplet size and rheological properties play a vital role in the quality of MEs. In this study, Non-ionic surfactants were used to formulate MEs containing ibuprofen. The MEs were characterized for their droplet size, poly disparity index (PDI), rheological properties. Furthermore, the flux of Ibuprofen was evaluated by Franz diffusion cell in-vitro over 24h where the penetrated amount of ibuprofen was estimated using high performance liquid chromatography (HPLC). The in-vivo bioavailabilities of encapsulated ibuprofen in MEs were studied in rats. The results showed that the MEs complies with their colloidal characteristics, transparency, and have ideal viscosity. Moreover, the highest achieved flux value of MEs containing ibuprofen through the skin using Franz diffusion cell was 0.039 mg/cm2 hr. The in vivo results showed a maximum plasma level 0.064 mg/ml at 8 hr for tested ME containing ibuprofen. The developed non-ionic MEs containing ibuprofen can be an ideal carrier and promising formulation for transdermal administration of ibuprofen.