Children with prenatal alcohol exposure (PAE) can have language, attention, and behavior problems. It is likely that altered brain function underlies these challenges, but no neuroimaging studies have examined brain function in young children with PAE, a time of critical development. Our study looked at how the brain works together as a network in young children with PAE (2-7 years) using functional magnetic resonance imaging (fMRI). We found that children with PAE had similar brain networks to children without PAE. However, brain networks in children with PAE developed differently. Over time, brain networks in children with PAE became more stable (i.e., less flexible), and more different from each other. But brain networks in children without PAE because more flexible and more similar to each other as they got older. This shows altered development of brain networks in young children with PAE, which may be related to their learning or behaviour problems.