Although delayed visual feedback to an action can reduce sense of agency, its effect on phantom motor sensation (i.e., sense of agency in phantom limb) has not been elucidated. We examined the effect of delayed visual feedback on phantom motor sensation in a male upper-limb amputee. In the experiment, he viewed video images of his intact right hand clasping and unclasping in a flat monitor placed in front of his left arm, and rated the intensity of phantom motor sensation. There were three delay conditions (0, 250, and 500 ms). Results showed that phantom motor sensation decreased when the image was delayed by 250 and 500 ms. However, when we instructed him to adjust the phase of phantom movement to that of the image with a 500-ms delay, phantom motor sensation increased. These results suggest that delayed visual feedback reduces phantom motor sensation, which is modulated by top-down effects.