In this paper, the problems of tracking control and finite-time stabilization of a high nonlinear system such as a robotic manipulator in the presence of actuator faults, uncertainties, and external disturbances are explored. In order to improve the performance of the system in the presence of actuator faults, uncertainties and external disturbances a novel fault tolerant control system based on fractional-order backstepping fast terminal sliding mode control is developed in this paper. The control system is developed by employing the results obtained from studies in the fields of fractional-order calculus, backstepping, sliding mode control, Mittag–Leffler stability, and finite-time Lyapunov stability. The performance of the suggested controller is then tested for a PUMA560 robot in which the first three joints are used. The simulation results validate the usefulness of the developed control approach in terms of accuracy of tracking, and convergence speed in the presence of disturbances, uncertainties and actuator faults. The trajectory tracking performance of the developed method is compared with other state of the art approaches such as conventional computed torque control, proportional integral derivative control and nonsingular fast terminal sliding mode control. The simulation results show that the proposed control approach performed better as compared to other control approaches in the presence of actuator faults, uncertainties, and disturbances.