This paper proposes a robust PD control scheme for flexible-joint robots based on a disturbance observer (DOB). In this paper, the DOB is applied only to the motor-side dynamics of the robot, and the uncertainties on the motor-side are successfully eliminated. It is shown that the proposed DOB-based approach guarantees global asymptotic stability. To this end, two special treatments are required. First, unlike the typical configuration of the DOB, nominal states of the motor-side are fed back to the PD controller. Second, a control input that makes the nominal states stable is additionally introduced. The proposed approach was verified using multi-degree-of-freedom experiments.