Within preterm-born children, being born male and at a lower gestational age (GA) have both been associated with a heightened risk for developmental difficulties. However, in this population little is known about the combined effect and the influence of these risk factors on cortical structures and executive control. In the present study, 58 preterm-born children (GA ranging from 24.0 to 35.1 weeks) were administered the computerized Child Attention Network Task at 6 years of age. Brain magnetic resonance imaging was performed and analyzed using Voxel-Based Morphometry (VBM) in all children. At a behavioral level, boys born <28 weeks of GA had significantly less executive control than preterm-born girls <28 weeks (p = .001) and preterm-born boys ≥28 (p = .003). The reduced executive control in preterm-born boys <28 weeks gestation was related to lower cortical densities in the inferior frontal gyrus (IFG) and dorsolateral prefrontal cortex (DLPFC). The current study links the higher incidence of reduced executive control in preterm-born boys to a higher degree of prematurity (low GA) and identifies brain structural abnormalities in the prefrontal cortex related to these deficits. The implications of these results are discussed.