Background: Externalising (delinquent, aggressive) and internalising (anxious/depressed, withdrawn) behaviour problems are prevalent in childhood. Few studies have prospectively measured relationships between childhood behaviour problems and adolescent health risk behaviour, a major predictor of morbidity and mortality. This study sought to determine relationships, by gender, between childhood behaviour problems and adolescent risky sexual behaviours and substance use. Methods: In a population-based birth cohort [The Western Australian Pregnancy Cohort (Raine) Study], total, externalising and internalising behaviour problems (domain-specific T>60) were calculated from parent-reported Child Behavior Checklist at ages 2, 5, 8, 10 and 14 years. At age 17 years, 1200 (49% male) participants reported sexual and substance use activity Results: For both genders, those with earlier externalising behaviour problems were more likely to be sexually active (oral sex or sexual intercourse) by age 17 years. Males with childhood externalising behaviour problems were more likely to have multiple sexual partners by age 17 years than those without such problems [adjusted odds ratio (aOR) 2.96, 95% confidence interval (CI) 1.49–5.86]. Females with childhood externalising behaviour problems were more likely to have had unwanted sex (aOR 1.91, 95% CI 1.04–3.53). Externalising behaviour problems were associated with substance use for both genders. No association was found between internalising behaviour problems and risky behaviour. Conclusions: Externalising behaviour problems from as early as 5 years old in boys and 8 years old in girls predict a range of risky sexual behaviour in adolescence, which has important implications for targeting interventions in adolescence.