We report here the first investigation of the effective connectivity between neural structures supporting attentional control using structural equation modeling and functional magnetic resonance imaging (fMRI). Attentional control was examined by employing a modified version of the flanker task. We found that the inconsistent condition elicited a significantly greater number of path coefficients than the consistent condition. In addition, we report that the strength of the prefrontal paths common to both conditions were not different, but that the remaining six paths were different between conditions. Importantly, these results suggest that the relationship between regions supporting attentional control differ between task conditions but the strength of the relationship between some prefrontal regions is invariant between task conditions. Additionally, we found that the paths were significantly lateralized to the right hemisphere. These results are discussed in relation to theories of the function of each region in attentional control.