This longitudinal prospective study examined the relation between maternal anxiety during pregnancy and specific aspects of children's cognitive functioning at age five. Antenatal maternal state-anxiety was measured around the 16th week of pregnancy. Children's neurocognitive functioning was examined using a simple reaction time (RT) task, and a choice RT task. Multiple regression analyses in the total sample (N = 922) showed that antenatal anxiety was positively related to children's intra-individual variability in RT in the simple task. In a subsample (n = 100) of women with state-anxiety scores above the 90th percentile, antenatal anxiety was positively associated with mean RT and intra-individual variability in RT in the incompatible trials of the choice RT task. In addition, in this subsample of highly anxious mothers we found a significant positive association in boys but not in girls, between prenatal maternal anxiety and intra-individual variability in RT in the simple task.