A detailed transport model for the Multitrack setup, a TAP-like system, has been developed, which allows further analysis of adsorption, diffusion and catalysis phenomena. This includes the transport in the void part between the pulse valve and the reactor inlet. The effects of viscous flow and thermal transpiration, aspects that have not been studied in detail before for this type of setup, have been analyzed. A new expression for the modeling of the output signal is proposed depending on the positioning of the MS detector used in the study. The transport parameters of the model have been estimated by the analysis of the experimental pulse responses of the empty reactor system and the reactor charged with an inert packed bed. The proposed model reproduces the experimental pulse responses very well, and therefore can be extended to study systems with reacting or adsorbing beds by including the corresponding rate equations for the processes occurring in the bed of particles.