Young people experiencing mental health conditions are vulnerable to poorer educational outcomes for many reasons, including: social exclusion, stigma, and limited in-school support. Using a near-complete New Zealand population administrative database, this prospective cohort study aimed to quantify differences in educational attainment (at ages 15–16 years) and school suspensions (over ages 13–16 years), between those with and without a prior mental health condition. The data included five student cohorts, each starting secondary school from 2013 to 2017 respectively (N = 272,901). Both internalising and externalising mental health conditions were examined. Overall, 6.8% had a mental health condition. Using adjusted modified Poisson regression analyses, those with prior mental health conditions exhibited lower rates of attainment (IRR 0.87, 95% CI 0.86–0.88) and higher rates of school suspensions (IRR 1.63, 95% CI 1.57–1.70) by age 15–16 years. Associations were stronger among those exhibiting behavioural conditions, compared to emotional conditions, in line with previous literature. These findings highlight the importance of support for young people experiencing mental health conditions at this crucial juncture in their educational pathway. While mental health conditions increase the likelihood of poorer educational outcomes, deleterious outcomes were not a necessary sequalae. In this study, most participants with mental health conditions had successful educational outcomes.