Using molecular dynamics (MD) simulations, binary mixtures of CF4 and either methane, ethane, butane, hexane, octane, or decane were studied in the zeolite faujasite. The results were analyzed to obtain the structural and transport properties of the system, primarily self-diffusivities and molecule sitings within the zeolite. The scaling of self-diffusivity with mixture composition was not pronounced for a given system and may be explained in terms of available volume and molecular mobility. Evidence of clustering of similar molecules was observed in systems with the longer alkane species. For methane-CF4 mixtures, the mutual transport diffusion coefficients were also calculated for equimolax mixtures. In all cases, the main-term transport diffusivities had larger values than their self-diffusivity counterparts. The cross-term diffusivities were an order of magnitude smaller than the main-term diffusivities. The main-term CF4 diffusivity and both cross-term diffusivities increased with loading, while the main-term methane diffusivity decreased with loading. The challenges involved in calculating the transport diffusivities for binary systems are discussed.