This study examined the long-term effects of a randomized controlled trial of the Family Check-Up (FCU) intervention initiated at age 2 on inhibitory control in middle childhood and adolescent internalizing and externalizing problems. We hypothesized that the FCU would promote higher inhibitory control in middle childhood relative to the control group, which in turn would be associated with lower internalizing and externalizing symptomology at age 14. Participants were 731 families, with half (n = 367) of the families assigned to the FCU intervention. Using an intent-to-treat design, results indicate that the FCU intervention was indirectly associated with both lower internalizing and externalizing symptoms at age 14 via its effect on increased inhibitory control in middle childhood (i.e., ages 8.5–10.5). Findings highlight the potential for interventions initiated in toddlerhood to have long-term impacts on self-regulation processes, which can further reduce the risk for behavioral and emotional difficulties in adolescence.