Repetitive transcranial magnetic stimulation (rTMS) is used to investigate normal brain function in healthy participants and as a treatment for brain disorders. Various subject factors can influence individual response to rTMS, including brain network properties. A previous study by our group showed that “virtually lesioning” the left dorsolateral prefrontal cortex (dlPFC; important for cognitive flexibility) using 1 Hz rTMS reduced performance on a set-shifting task. We aimed to determine whether this behavioural response was related to topological features of pre-TMS resting-state and task-based functional networks. 1 Hz (inhibitory) rTMS was applied to the left dlPFC in 16 healthy participants, and to the vertex in 17 participants as a control condition. Participants performed a set-shifting task during fMRI at baseline and directly after a single rTMS session 1–2 weeks later. Functional network topology measures were calculated from resting-state and task-based fMRI scans using graph theoretical analysis. The dlPFC-stimulated group, but not the vertex group, showed reduced setshifting performance after rTMS, associated with lower task-based betweenness centrality (BC) of the dlPFC at baseline (p =.030) and a smaller reduction in task-based BC after rTMS (p =.024). Reduced repeat trial accuracy after rTMS was associated with higher baseline resting state node strength of the dlPFC (p =.017). Our results suggest that behavioural response to 1 Hz rTMS to the dlPFC is dependent on baseline functional network features. Individuals with more globally integrated stimulated regions show greater resilience to rTMS effects, while individuals with more locally well-connected regions show greater vulnerability.