Self-regulation refers to the ability to monitor and modulate emotions, behavior, and cognition, which in turn allows us to achieve goals and adapt to ever changing circumstances. This trait develops from early infancy well into adulthood, and features both low-level executive functions such as reactive inhibition, as well as higher level executive functions such as proactive inhibition. Development of self-regulation is linked to brain maturation in adolescence and adulthood. However, how self-regulation in daily life relates to brain functioning in pre-adolescent children is not known. To this aim, we have analyzed data from 640 children aged 8–11, who performed a stop-signal anticipation task combined with functional magnetic resonance imaging, in addition to questionnaire data on self-regulation. We find that pre-adolescent boys and girls who display higher levels of self-regulation, are better able to employ proactive inhibitory control strategies, exhibit stronger frontal activation and more functional coupling between cortical and subcortical areas of the brain. Furthermore, we demonstrate that pre-adolescent children show significant activation in areas of the brain that were previously only associated with reactive and proactive inhibition in adults and adolescents. Thus, already in pre-adolescent children, frontal-striatal brain areas are active during self-regulatory behavior.