It is well known that Field Programmable Gate Arrays (FPGA) are good platforms for implementing embedded systems because of their configurable nature. However, the temperature of FPGAs is becoming a serious concern. Improvements in manufacturing technology led to increased logic density in integrated circuits as well as higher clock frequencies. As logic density increases, so do power density, which in turn increases the temperature, FPGAs follow the same path. A prediction of the thermal state of the Altera Cyclone V System-on-Chip (SoC) is presented in this work. The prediction study employs a numerical technique called Finite Element Method (FEM), which is a discretization method to approximate the real solution of the Partial Differential Equation (PDE) for heat transfer around the board's critical sources. The DE1 5CSEMA5F31C6N board was simulated using the COMSOL Multiphysics® tool for predicting thermal peaks during 13 hours of normal operation. Using the NISA tool, we obtained very similar results to those previously obtained with a margin of error of 2 %. As a result, a Verilog code implementation that describes the same approach used by the last two simulation tools is uploaded to the FPGA to verify the results of these simulations. This paper provides a more accurate vision of the level of operating stability of our FPGA board, which are currently the most important source for prototyping and designing the world's largest systems.