In this paper, thermo-elastic stress analysis of rotating variable thickness annular disk made of polar orthotropic functionally graded material (FGM) is presented. Elasticity modulus, density and thick-ness of the disk are assumed to vary radially according to a power law function. The material of the disk is assumed to be temperature dependent and different temperature distributions are assumed for variation of the temperature in radial direction. Radial stress and radial deformation of the disk with Clamped- Free (C-F) and Free-Free (F-F) boundary conditions are obtained using the numerical finite difference (FD) method. It is concluded that, by increasing the temperature variation, the radial stress and displacement increase. It is also observed that the radial stress in the rotating FG disk is more than the radial stress in rotating homogeneous disk and by increasing the FG index, the location of maximum stress in the disk shifts toward the outer surface. Also, the effects of temperature variation along the radius and orthotropy of the material on the radial stress and deformation are evaluated and concluded that their effect are significant. The results are compared with the available results in the literature and the good agreement between the present results and results in the literature shows the accuracy of FD method in thermo-elastic analysis of rotating FG orthotropic disk of variable thickness.