This paper presents a new control scheme for a flexible-joint manipulator using a higher-order differential feedback controller (HODFC). Two higher-order differential operators were designed and used to perform observations of both the reference input and the output of the manipulator, together with the requisite state derivatives. An error-based state-space model was then derived from the observed states. A pole-placement procedure with filtering was then used to drive the system error to zero. Practical controller implementation was carried out using the dSPACE real-time prototyping system. For the comparative validation of the performance of the HODFC with respect to a classical proportional-integral and proportional-integral-derivative (PID) controller, several experiments were undertaken. In these experiments, the step input, sine waves, kane trajectories, and external disturbances were applied to the controlled flexible-joint manipulator. The results showed that the HODFC controller eliminated disturbances within one second of occurrence, and produced superior kane trajectory tracking. Moreover, based on the root-mean-square tracking error criterion, the HODFC was observed to track both the sine and kane function trajectories with one-fourth the tracking error obtained with classical PID control.