Electronic components are normally assembled to printed circuit boards (PCBs). Such components generate heat in operation which must be conducted away efficiently from the small mounting areas to frames where the PCB is fixed. The temperature of the component depends on heat dissipation rate, technology and parameters of mounting, component placement and finally effective thermal conductivity (keff) of the board. The temperature of some components may reach significant magnitudes over 100°C while the PCB frame is kept at near-ambient temperature. The reliability of electronic components is directly related to operating temperature; so the thermal project should be able to provide a correct temperature prediction of all PCB components under the hottest operational condition. In space applications, the main way to spread and reject heat of electronic equipment is by thermal conduction once there is no air available to apply convection-based cooling techniques. The PCB keff is an important parameter for the electronics thermal analysis when the PCB is modeled as a simplified homogeneous board with a unique thermal conductivity. In this paper, an intrinsic uncertainty of such approach is firstly reveled and its magnitude is evaluated for a real space use PCB. The simulation uses SINDA/FLUINT Thermal Desktop and aims to determine the keff of the PCB by comparison between a detailed multi-layered anisotropic model and an equivalent homogeneous single-layer model. The model was validated using available data for two-layered FR4-copper PCB. Multiple simulations are performed with different dissipating component position and mounting area.