Continuous membrane separation of pharmaceuticals from an aqueous feed was studied theoretically by development of high-performance mechanistic model. The model was developed based on mass and momentum transfer to predict separation and removal of ibuprofen (IP) and its metabolite compound, i.e. 4-isobutylacetophenone (4-IBAP) from aqueous solution. The modeling study was carried out for a membrane contactor considering mass transport of solute from feed to organic solvent (octanol solution). The solute experiences different mass transfer resistances during the removal in membrane system which were all taken into account in the modeling. The model's equations were solved using computational fluid dynamic technique, and the simulations were carried out to understand the effect of process parameters, flow pattern, and membrane properties on the removal of both solutes. The simulation results indicated that IP and 4-IBAP can be effectively removed from aqueous feed by adjusting the process parameters and flow pattern. More removal was obtained when the feed flows in the shell side of membrane system due to improving mass transfer. Also, feed flow rate was indicated to be the most affecting process parameter, and the highest solute removal was obtained at the lowest feed flow rate.