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Reactive control of response inhibition is associated with a right-lateralised cortical network, as well as frontal-midline theta (FM-theta) activity measured at the scalp. However, response inhibition is also governed by proactive control processes, and how such proactive control is reflected in FM-theta activity and associated neural source activity remains unclear. To investigate this, simultaneous recordings of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) data was performed while participants performed a cued stop-signal task. The cues (0%, 25% or 66%) indicated the likelihood of an upcoming stop-signal in the following trial. Results indicated that participants adjusted their behaviour proactively, with increasing go-trial reaction times following increasing stop-signal probability, as well as modulations of both go-trial and stop-trial accuracies. Target-locked theta activity was higher in stop-trials than go-trials and modulated by probability. At the single-trial level, cue-locked theta was associated with shorter reaction-times, while target-locked theta was associated with both faster reaction times and higher probability of an unsuccessful stop-trial. This dissociation was also evident at the neural source level, where a joint ICA revealed independent components related to going, stopping and proactive preparation. Overall, the results indicate that FM-theta activity can be dissociated into several mechanisms associated with proactive control, response initiation and response inhibition processes. We propose that FM-theta activity reflects both heightened preparation of the motor control network, as well as stopping-related processes associated with a right lateralized cortical network.