<p>Low self-control in adults is associated with a broad range of negative outcomes. However, studies on the long-term impact of low self-control on mental health outcomes in youth are limited. We examined associations between low self-control during childhood (age 5–12) and mental health in adolescence (age 15–16), with specific interest for gender differences and whether conduct problems acts as a mediator.&#xa0;Data from a longitudinal birth cohort (Amsterdam Born Children and their Development) study was used (<i>n</i> = 1775). We scored self-control using items from the Strengths and Difficulties Questionnaire, Behavior Rating Inventory of Executive Function and Substance Use Risk Profile Scale collected at ages 5–6 and 11–12 years by multiple raters. Self-esteem (Rosenberg Self-esteem Scale), subjective well-being (Cantril-ladder), depression/anxiety symptoms (Youth Self Report) and perceived stress (Perceived Stress Scale) were mental health outcomes at age 15–16. We stratified by gender and tested mediation by conduct problem, as measured by the Strengths and Difficulties Questionnaire.&#xa0;Higher self-control was associated with higher self-esteem, higher subjective well-being, fewer depression/anxiety symptoms and less perceived stress in boys and girls (<i>p</i> &lt; 0.01). Overall, boys had lower self-control during childhood. Associations between self-control and mental health outcomes were stronger in girls than in boys. Conduct problems functioned as a (partial) mediator, but only in girls.&#xa0;Children with higher self-control had better mental health during adolescence, especially girls. In girls, conduct problems (partially) explained this association. Research is needed to find out if interventions, directed at enhancing self-control in childhood, are beneficial for later mental health.</p>