In this work, we investigate two recently synthesized naphthodithiophene diimide (NDTI) derivatives featuring promising n-type charge transport properties. We analyze the charge transport pathways and model charge mobility with the non-adiabatic hopping mechanism using the Marcus-Levich-Jortner rate constant formulation, highlighting the role of fluoroalkylated substitution in α (α-NDTI) and at the imide nitrogen (N-NDTI) position. In contrast with the experimental results, similar charge mobilities are computed for the two derivatives. However, while α-NDTI displays remarkably anisotropic mobilities with an almost one-dimensional directionality, N-NDTI sustains a more isotropic charge percolation pattern. We propose that the strong anisotropic charge transport character of α-NDTI is responsible for the modest measured charge mobility. In addition, when the role of thermally induced transfer integral fluctuations is investigated, the computed electron–phonon couplings for intermolecular sliding modes indicate that dynamic disorder effects are also more detrimental for the charge transport of α-NDTI than N-NDTI. The lower observed mobility of α-NDTI is therefore rationalized in terms of a prominent anisotropic character of the charge percolation pathways, with the additional contribution of dynamic disorder effects.