A nonlinear Time Delay Estimation (TDE) based model reference adaptive impedance controller was developed for Tarbiat Modares University Upper Limbs Rehabilitation Robot (TUERR). The proposed controller uses a stable reference impedance model, which produces desired dynamic relationship between applied force and position error for the robot End-effector to track the desired trajectory. TDE based model reference adaptive controller estimates unknown system dynamics and uncertainties, and the adaption law modifies the controller gains. Using a Lyapunov function was shown trajectory tracking errors in the overall system are bounded. In addition, a performance-based velocity profile proposed to modify the pace of trajectory planning considering the deviation from the desired path. Finally, the performance of the presented controller and rehabilitation process is experimentally investigated for TUERR.