Interhemispheric connections across the corpus callosum have a predominantly inhibitory effect. Previous electrophysiology studies imply that local inhibitory circuits are responsible for inducing transcallosal inhibition, likely through inhibitory GABAB-mediated neurotransmission. We investigated the neurochemical mechanisms involved in interhemispheric connectivity by measuring transcranial magnetic stimulation (TMS)-induced interhemispheric signal propagation (ISP) in the motor cortex and dorsolateral prefrontal cortex (DLPFC) with electroencephalography (EEG) recordings under the pharmacological effects of baclofen, l-DOPA, dextromethorphan, and rivastigmine. We hypothesized that for both stimulated regions, GABAB receptor agonist baclofen would decrease ISP when compared against baseline while drugs that target other neurotransmitter systems (dopaminergic, acetylcholinergic, and glutamatergic systems) would have no effect on ISP. Twelve right-handed healthy volunteers completed this study and underwent TMS across five sessions in a randomized order. In the motor cortex, participants showed a significant decrease in ISP under baclofen, but not in the other drug conditions. There were no drug-induced changes in ISP in the DLPFC and baseline ISP did not differ across experimental sessions for both brain regions. Together, our results suggest that the inhibitory effects observed with interhemispheric signal transmission are mediated by a population of interneurons involving GABAB receptor neurotransmission. Inhibitory mechanisms of ISP may be more salient for motor-related functions in the motor cortex than for cognitive control in the DLPFC. These findings are a fundamental step in advancing our understanding of interhemispheric connectivity and may be used to identify treatments for disorders in which transcallosal transmission is dysfunctional.