To examine associations between social relationships and school engagement in early secondary school and mental health, substance use, and educational achievement 2-4 years later. School-based longitudinal study of secondary school students, surveyed at school in Year 8 (13-14-years-old) and Year 10 (16-years-old), and 1-year post-secondary school. A total of 2678 Year 8 students (74%) participated in the first wave of data collection. For the school-based surveys, attrition was <10%. Seventy-one percent of the participating Year 8 students completed the post-secondary school survey. Having both good school and social connectedness in Year 8 was associated with the best outcomes in later years. In contrast, participants with low school connectedness but good social connectedness were at elevated risk of anxiety/depressive symptoms (odds ratio [OR]: 1.3; 95% confidence interval [CI]: 1.0, 1.76), regular smoking (OR: 2.0; 95% CI: 1.4, 2.9), drinking (OR: 1.7; 95% CI: 1.3, 2.2), and using marijuana (OR: 2.0; 95% CI: 1.6, 2.5) in later years. The likelihood of completing school was reduced for those with either poor social connectedness, low school connectedness, or both. Overall, young people's experiences of early secondary school and their relationships with others may continue to affect their moods, their substance use in later years, and their likelihood of completing secondary school. Having both good school connectedness and good social connectedness is associated with the best outcomes. The challenge is how to promote both school and social connectedness to best achieve these health and learning outcomes.