This paper describes a practical control scheme for autonomous capture of a free-flying satellite in space using an onboard manipulator. In capturing a satellite, a reference trajectory for control of a manipulator is generated with a time delay due to the processing time of a target motion estimator and a manipulator controller. Consequently, the control system shows poor performance and the end-effector sometimes fails to capture the target satellite. To solve this problem, a control system is proposed that utilizes predictive trajectory based on target satellite dynamics. The validity and usefulness of the proposed control method are shown by computer simulations and experiments using a 3-D hardware simulator with 9 degrees of freedom.