Children with Benign Epilepsy with Centrotemporal Spikes (BECTS), despite high likelihood for seizure remission, are reported to have subtle difficulties in language and other cognitive skills. We used functional MRI and a story listening task to examine the effect of BECTS on patterns of activation and connectivity. Language and cognitive skills were assessed using standardized measures. Twenty-four children with recently diagnosed BECTS and 40 typically-developing children participated. In a functionally-defined region of interest in right inferior frontal gyrus, BECTS patients showed a lower level of activation. Across both groups combined, increased activation in superior/middle temporal regions of interest was associated with better language scores. Connectivity in the story processing network was similar between groups, but connectivity within left inferior frontal gyrus was decreased in children with BECTS. These results suggest that language networks are largely maintained in new-onset BECTS, but some subtle changes in activation and connectivity can be observed.