Many processes have been identified in the Martian subsurface which may produce or release methane that eventually can be emitted into the atmosphere. Given the wide range of isotopic values for source carbon reported on Mars and the importance of atmospheric methane isotopologues as a tracer for subsurface processes, it is critical to quantify the level of isotopic fractionation that can occur during subsurface transport. On Earth, isotopic fractionation occurs when methane transport is dominated by Knudsen diffusion through small pores. However, unlike the Earth, on Mars the low atmospheric pressure and commensurate longer mean free path suggest that most subsurface transport of methane occurs in the Knudsen regime, amplifying this effect. Here, we report on simulations of diffusion through the martian subsurface and report on the level of fractionation that would be expected under two end-member scenarios. For Interplanetary Dust Particles (IDPs) incorporated in near-surface sediments in which methane is released quickly upon generation, atmospheric emissions of methane are expected to be representative of the reservoir isotopic ratio. However, for deeper sources in which methane accumulates as trapped gas, subsurface transport will result in depletions of 13CH4 compared to reservoir concentrations by approximately −31‰. Over time, both the reservoir and the emitted gas will evolve to become isotopically enriched in 13CH4 compared to a standard of constant isotopic ratio. This necessitates temporal measurements of emitted methane to understand the δ13C of the reservoir and depth of the release, preferably with hourly or better frequency. Finally, a seasonal cycle in δ13C with an amplitude of 5.3‰ is expected with adsorption acting to create small temporary reservoirs that are filled and emptied over the year by the subsurface thermal wave. This effect may provide a way to probe near-surface thermophysical properties.