This study was designed to optimize a fenofibrate-loaded self-microemulsifying drug delivery system (SMEDDS) by using a response surface methodology. Box–Behnken design (BBD) and its desirability function were used to optimize the SMEDDS. The independent factors were the amounts of Labrafil M 1944 CS, Labrasol, and Capryol PGMC and the dependent variables were droplet size, cumulative percentage of drug released in 30 min and equilibrium solubility of fenofibrate in SMEDDS. Various response surface graphs were used to understand the effects of each factor, and the desirability function was then adjusted to optimize SMEDDS formulation. The experimental values of optimized formulation were in close agreement with predicted values. Furthermore, in vivo pharmacokinetic study of the optimized formulation showed significant increase in relative oral bioavailability compared to that of the powder suspension. In conclusion, the BBD demonstrated its effectiveness in optimizing the SMEDDS formulation and in identifying the effects of formulation variables.