Carbon fibers can be considered cylindrically orthotropic. Depending on the arrangement of basal planes, predominant configurations are circumferential and radial, but in the core of the fiber, the alignment is undetectable, and consequently it is considered as transversely isotropic. In composites reinforced with these types of fibers, the effective thermal conductivity transverse to the fiber direction will be affected by the core and by the thermal resistance between the fiber and the matrix. The analytical models available are not adequate because they assume that the fiber is totally homogeneous. In this paper, a model of finite elements is presented, which allows combination of the effects of core with the cylindrical orthotropic of the fiber and the thermal contact resistance between the fiber and the matrix. The effective conductivity of composites with orthotropic and inhomogeneous fibers are compared to those with orthotropic and homogeneous fibers. This allows evaluation of the effect for the different morphology of the fibers. The model reveals a significant effect for radially orthotropic fibers (pitch-based). The model also contributes to a better understanding of the heat flux paths in cylindrically orthotropic and inhomogeneous fibers. Finally, this numerical simulation can be of interest first, in the microstructural studies focused on the relationship between the transverse thermal conductivity of carbon fibers and some microstructural parameters, and secondly, in the studies designed to estimate the interfacial contact resistance.