The mesoscopic framework describing single-component diffusion through microporous materials is extended here to characterize binary diffusion in the absence of intermolecular forces. Two diffusion mechanisms, single-file diffusion characteristic of confined pore structures and species-species exchange consistent with diffusion modes in less-confined pore topologies, are incorporated at the Master Equation level. Derived fundamentally via rigorous coarse-graining of the underlying Master Equation, the binary mesoscopic relation is validated via direct comparison to gradient continuous time Monte Carlo (G-CTMC) simulations. We further show the capability of this fundamentally derived model to capture the macroscopic diffusion phenomenon of ‘overshoot’ or ‘roll-up’ in the transient uptake and flux. Exploration of the species-species exchange mechanism reveals its strong effect on the transient ‘overshoot’ behavior through relaxation of the constrained single-file diffusion.