AbstractObjectiveThis study aimed to investigate the differences on resting‐state brain networks between the interictal epileptiform discharge (IED) group with self‐limited epilepsy with centrotemporal spikes (SeLECTS), the non‐IED group with SeLECTS, and the healthy control (HC) group.MethodsPatients were divided into the IED and non‐IED group according to the presence or absence of IED during magnetoencephalography (MEG). We used Wechsler Intelligence Scale for Children, fourth edition (WISC‐IV) to assess cognition in 30 children with SeLECTS and 15 HCs. Functional networks were constructed at the whole‐brain level and graph theory (GT) analysis was used to quantify the topology of the brain network.ResultsThe IED group had the lowest cognitive function scores, followed by the non‐IED group and then HCs. Our MEG results showed that the IED group had more dispersed functional connectivity (FC) in the 4–8 Hz frequency band, and more brain regions were involved compared to the other two groups. Furthermore, the IED group had fewer FC between the anterior and posterior brain regions in the 12–30 Hz frequency band. Both the IED group and the non‐IED group had fewer FC between the anterior and posterior brain regions in the 80–250 Hz frequency band compared to the HC group. GT analysis showed that the IED group had a higher clustering coefficient compared to the HC group and a higher degree compared to the non‐IED group in the 80–250 Hz frequency band. The non‐IED group had a lower path length in the 30–80 Hz frequency band compared to the HC group.ConclusionsThe study data obtained in this study suggested that intrinsic neural activity was frequency‐dependent and that FC networks of the IED group and the non‐IED group underwent changes in different frequency bands. These network‐related changes may contribute to cognitive dysfunction in children with SeLECTS.