Functionality of an open graded friction course (OGFC) depends on the high interconnected air voids or pores of the OGFC mixture. The authors' previous study indicated that the pores in the OGFC mixture were easily clogged by rutting deformation. Such a deformation-related clogging can cause a significant rutting-induced permeability loss in the OGFC mixture. The objective of this study was to control and reduce the rutting-induced permeability loss of the OGFC based on mixture design and layer thickness. Eight types of the OGFC mixtures with different air void contents, gradations, and nominal maximum aggregate sizes were fabricated in the laboratory. Wheel-tracking rutting tests were conducted on the OGFC slabs to simulate the deformation-related clogging. Permeability tests after different wheel load applications were performed on the rutted OGFC slabs using a falling head permeameter developed in the authors' previous study. The relationships between permeability loss and rutting depth as well as dynamic stability were developed based on the eight OGFC mixtures' test results. The thickness effects of the single-layer and the two-layer OGFC slabs were also discussed in terms of deformation-related clogging and the rutting-induced permeability loss. Results showed that the permeability coefficient decreases linearly with an increasing rutting depth of the OGFC mixtures. Rutting depth was recommended as a design index to control permeability loss of the OGFC mixture rather than the dynamic stability. Permeability loss due to deformation-related clogging can be effectively reduced by using a thicker single-layer OGFC or two-layer OGFC.