Sense of agency refers to the feeling of controlling one’s own body. Many patients surviving from a stroke lose the sense of agency over their body. This is due to impairments in both motor control and sensory brain functions. As a result of this lack in the sense of agency, stroke patients tend to lose the intention of moving the paralyzed limb, which results in further deterioration of brain functions and worsening muscles and joints. The present study proposes a motor rehabilitation system using virtual reality to improve the sense of agency during upper-limb movement which is required for various daily life activities such as eating meals and operating devices. Specifically, participants were instructed to move their hand to track a moving target ball in a virtual reality environment, while the position of their real hand was measured via a motion capture system. Participants were shown another ball presenting the position of their hand in virtual reality. We tested the proposed system with healthy participants, of which the motor control was disturbed by a 1-kg weight attached on the wrist. Participants reported their sense of agency after each trial. The results showed that the sense of agency was enhanced by the proposed intervention. Our results pointed out a potentially useful method to improve the sense of agency during body movements using modified visual feedback, which may contribute to the development of rehabilitation for stroke patients.