BACKGROUND: The ability to stop a suboptimal response is integral to decision making and is commonly impaired across psychiatric disorders. Cortical paired associative stimulation (cPAS) is a form of transcranial magnetic stimulation in which paired pulses can induce plasticity at cortical synapses. Here we used cPAS protocols to target cortico-cortical and cortico-subcortical networks by using different intervals between the paired pulses in an attempt to modify response inhibition. METHODS: A total of 25 healthy volunteers underwent four cPAS sessions in random order 1 week apart: right inferior frontal cortex (IFC) stimulation preceding right presupplementary motor area (pre-SMA) stimulation by 10 or 4 ms and pre-SMA stimulation preceding IFC stimulation by 10 or 4 ms. Subjects were tested on the stop signal task along with the delay discounting task as control at baseline (randomized across sessions and cPAS protocol) and after each cPAS session. RESULTS: The stop signal reaction time showed a main effect of cPAS condition when controlling for age (F3,57 = 4.05, p = .01). Younger subjects had greater impairments in response inhibition when the pre-SMA pulse preceded the IFC pulse by 10 ms. In older individuals, response inhibition improved when the IFC pulse preceded the pre-SMA pulse by 4 ms. There were no effects on delay discounting. CONCLUSIONS: cPAS modified response inhibition through age-dependent long-term potentiation and depression-like plasticity mechanisms via putative cortico-cortical and cortico-subcortical networks. We show for the first time the capacity for cPAS to modify a cognitive process highly relevant to psychiatric disorders.