An air gap membrane distillation (AGMD) system was applied for removal of benzene from benzene/water solution using polytetrafluoroethylene (PTFE) porous membrane. The experimental design using design methodology was applied for modeling and optimization of the process. The effects of air gap width and operation factors including feed temperature, concentration, flow rate, as well as their binary interactions on the permeation flux and separation factor were studied. Regression models, statistically validated by variance analysis, were developed to predict the AGMD performance. The optimum feed conditions for maximum separation were determined via D-optimal experimental design as temperature of 43 °C, concentration of 330 ppm, and flow rate of 3 mL/s at 5 mm air gap thickness.