The aim of this study was to investigate the neuropsychological profile of children with cryptogenic localization-related epilepsy (CLRE). Neuropsychological evaluations were performed in 16 CLRE children and 14 children with idiopathic localization-related epilepsy (ILRE) for control within 8 months (average 2.1 months) of initial seizure. The neuropsychological tests used in this study are as follows: the Wechsler Intelligence Scale for Children-Third Edition, Wechsler Intelligence Scale for Children-Revised, and Wechsler Preschool and Primary Scale of Intelligence. Age at onset and test differed significantly between CLRE and ILRE, while the duration between onset and test and the number of seizures before test did not. No marked difference was observed in the neuropsychological profile between 2 groups; however, the discrepancy between VIQ and PIQ was significantly larger in CLRE than in ILRE. This discrepancy was negatively correlated with age at the time of seizure onset (r = -0.615, and p = 0.011). The laterality in discrepancy between VIQ and PIQ was associated with the dominance of interictal discharge. In conclusion, children with lower age at the time of seizure onset were likely to have had a larger discrepancy between VIQ and PIQ.