A printed circuit board (PCB) is generally a multilayered board made of dielectric material and several layers of traces and vias. Performing detailed system-level computational fluid dynamics (CFD) simulations of PCBs including meshed trace and via geometries for each of the layers is impractical. In the present approach, the effects of the trace and via geometry are accurately modeled in the physical model by importing electronics computer aided-design data consisting of the trace and via layout of the board and computing locally varying orthotropic conductivity (kx, ky, and kz) on the printed circuit board using a background mesh. The spatially varying orthotropic conductivity is then mapped from the background mesh to the CFD mesh and used in a system-level simulation of the PCB with a minimal increase in the overall computational cost. On the other hand, as PCB component densities increase, the current densities increase thereby leading to regions of hot spots due to Joule heating. Hence, it is essential that the computational heat transfer simulations account for the heating due to the high current carrying traces. In order to accurately model the Joule heating of traces and vias, it is of essence to solve for the conservation of current in each of these traces. In this study, the effects of both trace layer nonhomogeneity and Joule heating are examined on a sample PCB with several components attached to it. The results are then compared with those from the conventional modeling techniques. It is demonstrated that there is considerable difference in the location of the hot spots and temperature values between two different methods.