Children with lower aerobic fitness have demonstrated worse performance on various cognitive tasks and differences in brain function compared to those with higher fitness. There is evidence that exercise improves cognitive function. This dissertation includes a series of three studies examining the effect of a randomized controlled exercise intervention on brain function and structure in overweight children. Participants in each study were subsets of individuals participating in the overall intervention study, who were unfit, overweight (body mass index ≥ 85th percentile) children 8-11 years old. Participants were randomly divided into either an aerobic exercise or attention control group. Each group was offered a separate instructor-led after-school program every school day for 8 months. Before and after the program, subsets of children participated in cognitive control tasks (antisaccade and flanker) during functional magnetic resonance imaging (fMRI), resting state fMRI, and/or diffusion tensor imaging (DTI). Changes over time in these measures were then compared between the exercise and control groups. Exercise altered brain activation during the cognitive control tasks. Specifically, the exercise group decreased activation in several brain regions related to antisaccade performance and increased activation in several regions related to flanker performance. During the resting state, exercise caused greater refinement of the default mode, cognitive control, and motor resting state networks compared to the control group. The motor network also showed an opposite pattern of increased synchrony with a frontal region. Finally, DTI data demonstrated a group by attendance interaction for white matter integrity such that attendance at the exercise intervention but not at the control group was associated with improved white matter integrity in the superior longitudinal fasciculus. In sum, exercise causes alterations in brain function during both cognitive control and a resting state in overweight children and is associated with alterations in white matter integrity in a tract supporting cognitive control. These results indicate that exercise improves the development of brain function and structure supporting cognitive control in overweight children.