A core feature of drug-resistant epilepsy is hyperexcitability in the motor cortex, and low-frequency repetitive transcranial magnetic stimulation is a suitable treatment for seizures. However, the antiepileptic effect causing network reorganization has rarely been studied. Here, we assessed the impact of rTMS on functional network connectivity in resting functional networks and their relation to treatment response. Fourteen patients with medically intractable epilepsy received inhibitive rTMS with a figure-of-eight coil over the vertex for 10 days spread across two weeks. We designed (...) a 6-week follow-up phase divided into four time points to investigate FNC and rTMS-induced timing-dependent plasticity, such as seizure frequency and abnormal interictal discharges on electroencephalography. For psychiatric comorbidities, the Hamilton Depression Scale and the Hamilton Anxiety Scale were applied to measure depression and anxiety before and after rTMS. FNC was also compared to that of a cohort of 17 healthy control subjects. The after-effects of rTMS included all subjects that achieved the significant decrease rate of more than 50% in interictal epileptiform discharges and seizure frequency, 12 patients with the reduction rate above 50% compared to the baseline, as well as emotional improvements in depression and anxiety. In the analysis of RSNs, we found a higher synchronization between the sensorimotor network and posterior default-mode network in epileptic patients than in healthy controls. In contrast to pre-rTMS, the results demonstrated a weaker FNC between the anterior DMN and SMN after rTMS, while the FNC between the aDMN and dorsal attention network was greater. Importantly, the depressive score was anticorrelated with the FNC of the aDMN-SMN, which was markedly different in the good and bad response groups treated with rTMS. Based on the vertex suppression by rTMS, it is possible to achieve temporary clinical efficacy by modulating network reorganization in the DMN and SMN for patients with refractory epilepsy. (shrink)