The objective of this study was to apply fractional factorial and multi-response optimization designs using desirability function approach for developing topical microemulsions. Minoxidil (MX) was used as a model drug. Limonene was used as an oil phase. Based on solubility, Tween 20 and caprylocaproyl polyoxyl-8 glycerides were selected as surfactants, propylene glycol and ethanol were selected as co-solvent in aqueous phase. Experiments were performed according to a two-level fractional factorial design to evaluate the effects of independent variables: Tween 20 concentration in surfactant system (X1), surfactant concentration (X2), ethanol concentration in co-solvent system (X3), limonene concentration (X4) on MX solubility (Y1), permeation flux (Y2), lag time (Y3), deposition (Y4) of MX microemulsions. It was found that Y1 increased with increasing X3 and decreasing X2, X4; whereas Y2 increased with decreasing X1, X2 and increasing X3. While Y3 was not affected by these variables, Y4 increased with decreasing X1, X2. Three regression equations were obtained and calculated for predicted values of responses Y1, Y2 and Y4. The predicted values matched experimental values reasonably well with high determination coefficient. By using optimal desirability function, optimized microemulsion demonstrating the highest MX solubility, permeation flux and skin deposition was confirmed as low level of X1, X2 and X4 but high level of X3.