We investigated the neural correlates of attentional modulation in the perceptual comparison process for detecting feature-binding changes in an event-related functional magnetic resonance imaging (fMRI) experiment. Participants performed a variant of a cued change detection task. They viewed a memory array, a spatial retro-cue, and later a probe array. Their task was to judge whether the cued item had changed between the two arrays. Change type was manipulated to be a color-location binding or a color feature change. The retro-cue onset time in the retention interval was manipulated to be early or late. As a consequence of strong inter-item competition, we found strong prefrontal activation for late cues when contrasting the binding-change with the color-change condition. In contrast, we observed a comparable behavioral and neural effect between the two types of change detection when retro-cue was presented early. More importantly, we demonstrated a significant inter-regional correlation between the prefrontal and parietal regions in both binding- and color-change conditions for late cues. In addition, extensive prefrontal–parietal–visual functional connectivity was showed for detecting binding changes in the late-cueing condition. These results support the critical role in prefrontal–parietal–visual functional coupling for resolving strong inter-item competition during the comparison process in the binding-change condition. We provide direct evidence that attention modulates neural activity associated with perceptual comparison, biasing competition in favour of the task-relevant information in order to detect binding changes.