In this study, a comparative study of two different hydrogen redistribution strategies along the Fischer-Tropsch synthesis reactor using a Pd-Ag membrane has been carried out. In the first strategy, fresh synthesis gas is flowing in the tube side in co-current mode with reacting material in shell side so that the first segments of reactor use more hydrogen. In the second strategy, fresh synthesis gas is flowing in the tube side in counter-current mode with reacting material in shell side so that last segments of reactor use more hydrogen. A one-dimensional heterogeneous model was developed to compare two strategies from different standpoints. The model was checked using operating data of Fischer-Tropsch synthesis reactor in pilot plant of Research Institute of Petroleum Industry in Iran. Simulation results show an enhancement in the yield of gasoline production, a decrease in undesired products formation (CO 3 and CH 4 ) and also a favorable temperature profile along both the configurations of membrane Fischer-Tropsch reactor in comparison with conventional reactor. The comparison between co-current and counter-current configurations in terms of temperature, gasoline (C 5 1 ) and CO 2 yields, H 2 and CO conversions, and selectivity of components shows the reactor in the co-current configuration operates with lower reactants' conversions and also lower permeation rate of hydrogen. On the contrary, our results demonstrated counter-current-mode decrease CO 2 and CH 4 as undesired products, better than other kinds of mentioned systems.