Brain and heart development occurs simultaneously in the fetus with congenital heart disease. Early morphogenetic programs in each organ share common genetic pathways. Brain development occurs across a more protracted time-course with striking brain growth and activity-dependent formation and refinement of connections in the third trimester. This development is associated with increased metabolic activity and the brain is dependent upon the heart for oxygen and nutrient delivery. Congenital heart disease leads to derangements of fetal blood flow that result in impaired brain growth and development that can be measured with advanced magnetic resonance imaging. Delayed development results in a unique vulnerability to cerebral white matter injury in newborns with congenital heart disease. Delayed brain development and acquired white matter injury may underlay mild but pervasive neurodevelopmental impairment commonly observed in children following neonatal congenital heart surgery.