Despite trends indicating worsening internalizing problems, characterized by anxiety and depression, there is dearth of research examining gender differences in developmental trajectories of internalizing problems from early childhood to adolescence. Drawing on the UK Millennium Cohort Study (n = 17,206, 49% female), this study examines trajectories of parent-reported, clinically-meaningful (reflecting the top 10%) internalizing problems from ages 3 to 14 years and their early predictors and adolescent outcomes. Group-based modelling revealed three trajectories when examining boys and girls together, but there were significant gender differences. When examining boys and girls separately, four trajectories were identified including two relatively stable trajectories showing either high or low probabilities of internalizing problems. An increasing trajectory was also found for both boys and girls, showing an increasing probability of internalizing problems which continued to rise for girls, but levelled off for boys from age 11. A decreasing trajectory was revealed for boys, while a moderate but stable trajectory was identified for girls. Boys and girls in the increasing and high probability groups were more likely to report a number of problematic outcomes including high BMI, self-harm, low mental wellbeing, depressive symptoms, and low educational motivation than the low group. Girls on the increasing trajectory also reported more cigarette and cannabis use and early sexual activity at age 14 compared to girls on the low trajectory. Findings suggest that intervention strategies take a systemic view, targeting not only internal feelings, but also behaviours potentially associated with later negative outcomes.