The prefrontal cortex (PFC) is thought to modulate the neural network state in favor of the processing of task-relevant sensory information prior to the presentation of sensory stimuli. However, this proactive control mechanism cannot always optimize the network state because of intrinsic fluctuation of neural activity upon arrival of sensory information. In the present study, we have investigated an additional control mechanism, in which the control process to regulate the behavior is adjusted to the trial-by-trial fluctuation in neural representations of sensory information. We asked normal human subjects to perform a variant of the Stroop task. Using functional magnetic resonance imaging, we isolated cognitive conflict at a sensory processing stage on a single-trial basis by calculating the difference in activation between task-relevant and task-irrelevant sensory areas. Activation in the dorsolateral PFC (DLPFC) covaried with the neural estimate of sensory conflict only on incongruent trials. Also, the coupling between the DLPFC and anterior cingulate cortex (ACC) was tighter on high-sensory conflict trials with fast response. The results suggest that although detection of sensory conflict is achieved by the DLPFC, online behavioral adjustment is achieved by interactive mechanisms between the DLPFC and ACC.