To efficiently deal with quickly changing task demands, we often need to organize our behaviour on different time scales. For example, to ignore irrelevant and select relevant information, cognitive control might be applied in reactive (short time scale) or proactive (long time scale) mode. These two control modes play a pivotal role in cognitive-neuroscientific theorizing but the temporal dissociation of the underlying neural mechanisms is not well established empirically. In this fMRI study, a cognitive control task was administered in contexts with mainly congruent (MC) and mainly incongruent (MI) trials to induce reactive and proactive control, respectively. Based on behavioural profiles, we expected cognitive control in the MC context to be characterized by transient activity (measured on-trial) in task-relevant areas. In the MI context, cognitive control was expected to be reflected in sustained activity (measured in the intertrial interval) in similar or different areas. Results show that in the MC context, on-trial transient activity (incongruent – congruent trials) was increased in fronto-parietal areas, compared to the MI context. These areas included dorsolateral prefrontal cortex (dlPFC) and intraparietal sulcus (IPS). In the MI context, sustained activity in similar fronto-parietal areas during the intertrial interval was increased, compared to the MC context. These results illuminate how context-dependent reactive and proactive control subtend the same brain areas but operate on different time scales.