Benign childhood epilepsy with centrotemporal spikes (BECTS) is one of the most common childhood epilepsy syndromes and may be associated with language deficits. Resting-state functional magnetic resonance imaging (fMRI) data were collected from a total of 78 children: 52 patients with BECTS (28 drug-naïve and 24 medicated) and 26 healthy controls (HC). Granger causality analysis (GCA) was used to investigate alterations in effective connectivity (EC) between the language network core node (Broca's area) and the whole brain. EC from Broca's area to the left Heschl's gyrus (HG), right putamen, and anterior cingulate cortex (ACC) was significantly increased, while EC from the bilateral putamen and left ACC to Broca's area was significantly decreased in BECTS. Moreover, altered EC of Broca's area to the right putamen was significantly positively correlated with verbal IQ (VIQ), while altered EC of Broca's area to the ACC showed significantly negative correlations with the frequency of seizures. Altered EC from the left putamen to Broca's area was also significantly negatively correlated with performance IQ (PIQ) and full-scale IQ (FSIQ) in the drug-naïve group. In addition, there was a significant positive correlation between the EC of Broca's area to the left HG and the number of seizures, as well as between the EC of Broca's area to the right putamen and the age at onset in the medicated group. These findings suggest abnormal causal effects on the language network related to Broca's area in children with BECTS. Longitudinal investigation of language network development and further follow-up may be needed to illuminate the changes in organization and rebalancing over time.