Benign epilepsy with centrotemporal spikes (BECT) is the most common childhood idiopathic focal epilepsy syndrome, which characterized with white‐matter abnormalities in the rolandic cortex. Although diffusion tensor imaging research could characterize white‐matter structural architecture, it cannot detect neural activity or white‐matter functions. Recent studies demonstrated the functional organization of white‐matter by using functional magnetic resonance imaging (fMRI), suggesting that it is feasible to investigate white‐matter dysfunctions in BECT. Resting‐state fMRI data were collected from 24 new‐onset drug‐naive (unmedicated [NMED]), 21 medicated (MED) BECT patients, and 27 healthy controls (HC). Several white‐matter functional networks were obtained using a clustering analysis on voxel‐by‐voxel correlation profiles. Subsequently, conventional functional connectivity (FC) was calculated in four frequency sub‐bands (Slow‐5:0.01–0.027, Slow‐4:0.027–0.073, Slow‐3:0.073–0.198, and Slow‐2:0.198–0.25 Hz). We also employed a functional covariance connectivity (FCC) to estimate the covariant relationship between two white‐matter networks based on their correlations with multiple gray‐matter regions. Compared with HC, the NMED showed increased FC and/or FCC in rolandic network (RN) and precentral/postcentral network, and decreased FC and/or FCC in dorsal frontal network, while these alterations were not observed in the MED group. Moreover, the changes exhibited frequency‐specific properties. Specifically, only two alterations were shared in at least two frequency bands. Most of these alterations were observed in the frequency bands of Slow‐3 and Slow‐4. This study provided further support on the existence of white‐matter functional networks which exhibited frequency‐specific properties, and extended abnormalities of rolandic area from the perspective of white‐matter dysfunction in BECT.