Abstract Background Sub-optimal functioning of the dorsal prefrontal cortex (PFC) is associated with executive dysfunction, such as set-shifting deficits, in neurological and psychiatric disorders. We tested this hypothesis by investigating the effect of low-frequency ‘inhibiting’ off-line repetitive transcranial magnetic stimulation (rTMS) on the left dorsal prefrontal cortex on behavioural performance, neural activity, and network connectivity during the performance of a set-shifting paradigm in healthy elderly (mean age 50+). Results Behaviorally, we found a group-by-session interaction for errors on set-shift trials, although post hoc tests did not yield significant findings. In addition, the verum group, when compared with the sham group, displayed reduced task-related activity in the left temporal gyrus, and reduced task-related connectivity of the left PFC with the left postcentral gyrus and posterior insula. Conclusion These results show that low-frequency off-line rTMS on the left dorsal PFC resulted in reduced task-related activity and network connectivity, which was accompanied by a subtle behavioural effect, thereby further corroborating the importance of an optimally functioning PFC in set-shifting.