This study examined whether physical activity, mental health and socio-economic position were associated with the overall academic performance and future educational plans of adolescents aged 15-16 years. We used a sample of 7002 boys and girls from the Northern Finland Birth Cohort 1986. Data were collected by a postal enquiry in 2001-02. Multivariable logistic regression models were estimated and adjusted for family structure and all variables in the models. In the fully adjusted models, higher levels of physical activity and high parental socio-economic position were associated with higher overall academic performance and future plans for higher education. High scoring on behavioural problems was related to lower overall academic performance and poorer future academic plans. In summary, a higher level of physical activity, fewer behavioural problems and higher socio-economic position were independently associated with high self-perceived overall academic performance and plans for higher education among adolescents. The interrelations of these factors and the positive relationship between physical activity, mental health and school outcomes provide a context of critical importance for future research, intervention programming and policy directed at improving the educational attainment of adolescents.