Sex differences in cognitive functioning were investigated in children with velocardiofacial syndrome (VCFS), a genetic defect caused by a microdeletion on chromosome 22q.11. The study population consisted of six groups: 50 boys with VCFS (M = 11.1, SD = 2.7), 40 girls with VCFS (M = 10.8, SD = 2.5), 13 male siblings of the participant with VCFS (M = 12.3, SD = 1.9), 17 female siblings of the participant with VCFS (M = 12.2, SD = 1.9), and a race- and gender-ratio-matched sample of 28 boy community control participants (M = 10.7, SD =2.4) and 19 girl community control participants (M = 9.2, SD =2.3). Each participant received a psychological assessment including intellectual and academic achievement as well as structural magnetic resonance imaging of his or her brain. Our results indicate that boys with VCFS may be more cognitively affected than girls. In addition, and although cross-sectional in nature, our results document a negative association between age and cognitive functioning in girls with VCFS but not in boys. Sex differences in frontal lobe volume are generally seen in the general population between boys and girls (boys > girls) and across all three samples, this trend emerged. Relative to boys with VCFS, girls with VCFS may be less cognitively affected, although age is negatively associated with cognitive functioning in girls with VCFS but not boys, suggesting that girls with VCFS may fail to maintain this cognitive advantage over boys.