Our work is aimed at exploring the composition and the properties of microemulsion (ME), as a drug delivery system, to enhance the permeability across the gastrointestinal (GI) barrier of fenofibrate, a BCS class II drug. It is a prodrug that is converted rapidly after oral administration into a major active metabolite which is the fenofibric acid. It undergoes a nearly complete presystemic metabolism. Its main drawback is the low bioavailability of the metabolite. A quick selection of excipients was made based on the capacity of solubilization and the value of hydrophilic-lipophilic balance. The classical method of ME development was coupled with the factorial design in order to minimize the droplet size using a low concentration of surfactant. The optimized ME showed a droplet size of 48.5 nm and physical stability. The passive permeability evaluated using Sartorius was 1.6 times higher than that of the free drug. The ex vivo technique, performed using the everted gut sac model, showed a 2.5-fold higher permeability. This suggests that the carrier-mediated uptake/efflux may present the dominant transport mechanism of fenofibrate. The use of the excipients that inhibit GI P-glycoprotein may be a new perspective. Thus, this paper shows that the composition and the characteristics of ME may be explored to increase the permeability of fenofibrate across the GI membrane.