The trajectory tracking in the flexible-joint manipulator (FJM) system becomes complicated since the flexibility of the joint of the FJM superimposes vibrations and non-minimum phase characteristics. In this paper, a distributed higher-order differential feedback controller (DHODFC) using the link and joint position measurement was developed to reduce joint vibration in step input response and to improve tracking behavior in reference trajectory tracking control. In contrast to the classical higher-order differential (HOD), the dynamics of the joint and link are considered separately in DHODFC. In order to validate the performance of the DHODFC, step input, trajectory tracking, and disturbance rejection experiments are conducted. In order to illustrate the differences between classical HOD and DHODFC, the performance of these controllers is compared based on tracking errors and energy of control signal in the tracking experiments and fundamental dynamic characteristics in the step response experiments. DHODFC produces better tracking errors with almost same control effort in the reference tracking experiments and a faster settling time, less or no overshoot, and higher robustness in the step input experiments. Dynamic behavior of DHODFC is examined in continuous and discontinues inputs. The experimental results showed that the DHODFC is successful in the elimination of the nonminimum phase dynamics, reducing overshoots in the tracking of such discontinuous input trajectories as step and square waveforms and the rapid damping of joint vibrations.