It is well known that performance on a trial is flexibly modulated by preceding trial congruency in tasks that require cognitive control, such as the Stroop task, referred to as the conflict adaptation effect (CAE). The CAE indicates that conflict on the preceding trial leads to enhanced cognitive control, leading to more efficient regulation of current conflict. The present study aimed to identify neural mechanisms implicated in individual differences in CAEs. The participants performed a version of the color-word Stroop task during a functional magnetic resonance imaging (fMRI) experiment and were divided into two groups according to the magnitude of behavioral CAE: one exhibiting the CAE only in congruent trials and the other in both congruent and incongruent trials. The imaging results showed different activations in the pre-supplementary motor area for the Stroop effect between groups. Importantly, group differences in activation for the preceding trials were observed in several prefrontal regions including the bilateral frontopolar, dorsolateral prefrontal, and rostro-dorsal cingulate cortices. More interestingly, analyses of the preceding trials suggest that the frontopolar cortex is involved in conflict resolution through higher-order cognitive control strategies that are closely associated with subsequent conflict. The current study provides new evidence of the role of the frontopolar cortex in conflict adaptation.