While there are theoretical arguments that suggest school practices can exacerbate delinquent behaviour by youth, research has not consistently examined this potential of schools to contribute to poorer outcomes for the most at-risk youth in our communities. This paper uses longitudinal data (n = 495) to examine the role being excluded from school plays in later criminal justice involvement for a group of at-risk youth in New Zealand. Path analysis is used to explore the interaction of contextual and personal risks as well as educational resources (Time 1) on personal and peer risks (Time 2), and engagement with Youth Criminal Justice (Time 3), accounting for differences between males and females using a multi-group analysis. Between groups t-tests were used to further understand the differences between genders. A direct link between being excluded from school and later criminal justice involvement is found, with an indirect link via delinquency (Time 2). Similar factors influence male and female pathways from school to prison, but their relative influence differs by gender: among youth interviewed, females reported higher rates of exclusion, while males reported receiving greater academic support, although this support did not reduce justice system involvement. Results highlight the need for educational programmes and policies to address underlying causes of delinquent behaviour if the pathway from school exclusion to the justice system is to be removed. Such policies and programmes need to target children early, promote the development of positive supportive relationships with teachers that can mitigate risks and provide opportunities for youth to build pro-social peer relationships.