Despite the outstanding chemical, thermal and transport properties of amorphous and glassy perfluorinated polymers, only few works exist on the preparation and transport properties of perfluoropolymer/molecular sieves mixed-matrix membranes (MMMs), probably because of their poor compatibility. In this review, the compatibilization of ceramic molecular sieves with perfluorinated matrices is considered first, examining the effect of the surface treatment on the gas transport properties of the filler. Then the preparation of the defect-free hybrid membranes and their gas separation capabilities are described. Finally, recent modelling of the gas transport properties of the perfluoropolymer MMMs is reviewed. The systematic use of molecular sieves of different size and shape, either permeable or impermeable, and the calculation of the bulk transport properties of the molecular sieves—i.e., the unrestricted diffusion and permeability—allow to understand the nature of the physical phenomena at work in the MMMs, that is the larger the perfluoropolymer fractional free volume at the interface, and restricted diffusion at the molecular sieves. This knowledge led to the formulation of a new four-phase approach for the modelling of gas transport. The four-phase approach was implemented in the frame of the Maxwell model and also for the finite element simulation. The four-phase approach is a convenient representation of the transport in MMMs when more than one single interfacial effect is present.