Background and purpose: Although benign childhood epilepsy with centrotemporal spikes (BECTS) is known to have good prognosis, patients often manifest neuropsychological impairments. This study aimed to investigate cognitive dysfunctions and their relationship with white matter microstructural changes in BECTS patients. Methods: Nineteen BECTS and 25 normal subjects aged 7–16 years were included. Neuropsychological performances were assessed by the Wechsler Intelligence Scale for Children III, executive function tests, verbal and visuospatial memory tests, the verbal fluency and Boston naming tests. Diffusion tensor imaging (DTI) was performed to measure the fractional anisotropy (FA), axial (AD), radial (RD), and mean diffusivities (MD). The voxel-wise tract-based spatial statistics and region of interest methods were used for DTI, and their correlations with cognitive variables were analyzed. Results: Patients with BECTS had lower intelligence quotient (IQ) scores compared with those of the control group. Higher AD and MD values were found in the left superior longitudinal fasciculus, the retrolenticular part of the internal capsule, posterior thalamic radiation, sagittal stratum and the body of the corpus callosum in BECTS patients compared with controls. Lower performances in verbal IQ, freedom from distractibility and processing speed were correlated with higher AD in the left superior fronto-occipital fasciculus, and lower verbal IQ scores were correlated with decreased FA values in the splenium of the corpus callosum in these patients. Conclusions: White matter microstructural changes predominantly in the left hemisphere might contribute to their cognitive abnormalities especially verbal IQ in BECTS patients.