Previous studies have established a role for premotor cortex in the processing of auditory emotional vocalizations. Inhibitory continuous theta burst transcranial magnetic stimulation (cTBS) applied to right premotor cortex selectively increases the reaction time to a same-different task, implying a causal role for right ventral premotor cortex (PMv) in the processing of emotional sounds. However, little is known about the functional networks to which PMv contribute across the cortical hemispheres. In light of these data, the present study aimed to investigate how and where in the brain cTBS affects activity during the processing of auditory emotional vocalizations. Using functional neuroimaging, we report that inhibitory cTBS applied to the right premotor cortex (compared to vertex control site) results in three distinct response profiles: following stimulation of PMv, widespread frontoparietal cortices, including a site close to the target site, and parahippocampal gyrus displayed an increase in activity, whereas the reverse response profile was apparent in a set of midline structures and right IFG. A third response profile was seen in left supramarginal gyrus in which activity was greater post-stimulation at both stimulation sites. Finally, whilst previous studies have shown a condition specific behavioral effect following cTBS to premotor cortex, we did not find a condition specific neural change in BOLD response. These data demonstrate a complex relationship between cTBS and activity in widespread neural networks and are discussed in relation to both emotional processing and the neural basis of cTBS.