Rotational elastic instability of annular members is an important phenomenon which may lead to the destruction of structures. The instability analysis of rotating disks made of carbon nanotube reinforced composite (FG-CNTRC) has been presented. This study is the first to investigate the rotational instability of FG-CNTRC disks, providing new insights into the design of high-stability rotating structures. The rotating disk mounted to rigid shaft has variable-thickness and the function of CNT distribution along the radial coordinate may be uniform or functionally graded. The refined rule of mixture approach is used to obtain the material properties of composite where efficiency parameters are considered. The actual centrifugal force with radial displacement is taken into account and the burst velocities at which instability observed are obtained. The theory used in the analysis is plane elasticity and the governing differential equations of the problem have variable-coefficients where the analytical solution may not be available. Complementary Functions Method, which is a powerful numerical solution scheme, is implemented into the analysis and high accuracy with few collocation points are achieved using non-dimensional parameters. The influences of CNT distribution pattern, volume fraction of CNTs and variations of thickness profiles on the burst velocities of disk are examined. It is revealed that CNT addition to the isotropic polymer has a stabilizing effect on the rotating disk by increasing the burst velocity and the most effective parameter is the CNT distribution pattern. Considering all distribution patterns, the FG-V pattern yields the most stable disk design. Validation of the results is done using analytical solution which is only available for uniformly distributed CNTRC with the hyperbolic thickness profile.