The present study used functional magnetic resonance imaging (fMRI) and a cued version of a flanker paradigm to elucidate the effects of task preparation on subsequent brain activation patterns. A mixed block and event-related design was employed to examine activations associated with the cue periods themselves and the cued and un-cued correct responses to incongruent flankers. A number of areas were active during the cues, most notably left dorsolateral prefrontal cortex (DLPFC), which was interpreted as subserving a role in task-set maintenance. Widespread activity was noted for correct responses to incongruent flankers, including bilateral parietal and frontal regions, consistent with previous studies. Activation was increased in these regions for correct responses after cue periods. An overlapping network of regions was also noted for cues and correct responses, suggesting preparation of task-appropriate anatomical regions during the cue period. These results suggest that cue periods allow participants to prime task-relevant areas within the brain and highlight the importance of left DLPFC in top-down control.