Considerable evidence indicates that a stimulus that is subthreshold, and thus consciously invisible, influences brain activity and behavioral performance. However, it is not clear how subthreshold stimuli are processed in the brain. We found that a task-irrelevant subthreshold coherent motion led to a stronger disturbance in task performance than did suprathreshold motion. With the subthreshold motion, activity in the visual cortex measured by functional magnetic resonance imaging was higher, but activity in the lateral prefrontal cortex was lower, than with suprathreshold motion. These results suggest that subthreshold irrelevant signals are not subject to effective inhibitory control.