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A critical function of executive control is the ability to flexibly inhibit or change a plan of action when it is contextually inappropriate. Using human fMRI and a context-dependent stop signal task (SST), we found a functional double dissociation between the right ventrolateral prefrontal cortex (rVLPFC) and the bi-lateral frontal eye field (FEF). rVLPFC activation was associated with detecting and encoding the meaning of stop signals and the response inhibition, while FEF activity reflected motor output regardless of the stimulus response mapping or the context. Furthermore, a representation of stop signal meaning and response inhibition were represented in separate regions of rVLPFC. These results were further validated by electrophysiological recordings in rVLPFC and FEF from one monkey. The findings suggest that inhibition of a planned behavior is not governed by a single brain system as had been previously proposed, but instead depends on two neurally distinct processes.