Difficulties in regulating affect are core characteristics of a wide range of mental health conditions and are associated with deficits in cognitive control, particularly in affective contexts, affective control. The current study explored how affective control relates to mental health over the course of adolescence. We developed an Affective Control Task, which was administered to young adolescents (11–14 years; n = 29); mid-adolescents (15–18 years; n = 31), and adults (22–30 years; n = 31). The task required individuals to sort cards according to continuously changing rules: color, number, or item type. There was a neutral condition in which items were shapes, and an affective condition, in which items were emotional facial expressions. Better affective control was associated with fewer mental health difficulties (p < .001, R2 = .15). Affective control partially accounted for the association between age group and mental health problems, z = 2.61, p = .009, Akaike information criterion = 484, with the association being strongest in young adolescents, r (27) = −.44, p = .018. Affective control further accounted for variance in the association between self-reported (but not experimental) emotion regulation and mental health (z = −3.44, p < .001, Akaike information criterion = 440). Poor affective control, especially in young adolescents, is associated with more mental health problems and higher levels of emotion regulation difficulties. Improving affective control therefore may constitute a promising target for prevention.