Three-dimensional Finite Element (FE) analysis has been carried out using ANSYS software to study the natural frequencies of functionally graded (FG) rotor system. Temperature and position-dependent material properties of the FG shaft system are considered to be graded in the radial direction. Power-law with the nonlinear temperature distribution (NLTD) and exponential law with exponential temperature distribution (ETD) have been used to model the material gradation and temperature distribution. Rotor systems of two different FG materials, namely Stainless Steel-ZrO2 and Stainless Steel-Al2O3 have been studied. Python codes have been developed to generate ANSYS macros that apply the material properties. Simply supported FG shaft and FG rotor system supported on bearings have been analyzed in the current work. The results show the influence of different power-law coefficients, different material and material laws on the natural frequencies of the rotor system. The effect of these parameters on whirl frequencies has also been studied for FG rotor systems.