The simulation of fermentation product separation using nanoporous membranes is presented. The aim of the simulation was to predict the performance of an extraction process to remove compounds from aqueous solutions. The simulation was conducted using computational fluid dynamics techniques for the solution of governing equations. The system studied was a membrane-based extractor of acetone from aqueous solutions using near-critical CO2 as solvent. The predicted extraction percentages obtained by the simulations were compared to experimental values reported in the literature and showed very good agreement. The simulation can predict the concentration profile of acetone in the membrane and also predicts the formation of a concentration boundary layer.