Charge transport in a naphthalene π-stack system can exhibit switching because of variation in its redox state. We study this phenomenon in a molecular π-stack with the aim of obtaining insight into the charge transport in DNA solid-state devices. The model molecular π-stack is based on the structure of naphthalene tetracarboxylic diimide (NTCDI), which is assembled by molecular layer epitaxy (MLE). MLE enables controllable growth of two-dimensional organic frameworks featuring ordered π-stacked arrays of aromatic molecules. These molecular stacks are grown in the in-plane direction with respect to the surface and are bonded covalently to the inorganic semiconducting substrate. In this system, the reduced NTCDI acceptors form redox polarons in which the charge is shared over several molecules within the π-stack. We study the experimental conditions that are required to sustain efficient transport in this redox-capable NTCDI molecular π-stack. The transport in this redox-active system follows the behavior of the polarons. Polaron transport occurs below the HOMO–LUMO gap in a molecular system, for which either ln I ∼ −E−2/3 or I ∼ E (linear regime). We also study the case of redox blockade for the NTCDI molecular π-stack. We demonstrate that the same model (i.e., ln I ∼ −E−2/3) is applicable for transport through DNA molecules positioned between nano-electrodes. Studying the transport in a molecular π-stack enables elucidation of the phenomenon of conductivity switching, which may be responsible for the discrepancies among different transport experiments with DNA solid-state devices. We propose a generalized-effective-medium approach to describe the redox polaron transport in a molecular stack, an approach that is based on a fully compensated semiconductor model.