This paper proposes a saturated output feedback controller for flexible-joint robot manipulators with joints of arbitrary flexibility. First, under the framework of singular perturbation theory, a saturated flexible compensator is introduced in the dynamics model to enlarge the joint stiffness and achieve a united control for the robot with joints of arbitrary flexibility. Meanwhile, the saturation problem of torque control is also addressed. Second, an extended Kalman filter (EKF) with adaptive high gain that combines the noise filter of EKF with global convergence of high-gain observer is presented to enable the output feedback tracking control without the velocity of the link side or the motor side. Third, explicit but strict stability analyses of the whole system in both full-state feedback and output feedback are given. Finally, simulation comparisons are provided to verify the effectiveness of the proposed approach.