This study examined how schools prioritize ten key health concerns among their student populations over time and whether schools' prioritization of alcohol and other drug use (AODU) corresponds to students' substance use behaviours and cannabis legalization as a major policy change. Data were collected from a sample of secondary schools in Ontario, Canada across four years (2015/16-2018/19 [N[superscript 2015/16] = 65, N[superscript 2016/17] = 68, N[superscript 2017/18] = 61 and N2018/19 = 60]) as a part of the COMPASS study. School-level prevalence of cannabis and alcohol use between schools that did and did not prioritize student AODU as a health concern was examined. Ordinal mixed models examined whether student cannabis and alcohol use were associated with school prioritization of AODU. Chi-square tests examined changing health priorities among schools pre-post cannabis legalization. School priority ranking for AODU was mostly stable over time. While AODU was identified as an important health concern, most schools identified mental health as their first priority across the four years of the study. No significant changes to school AODU priorities were observed pre--post cannabis legalization nor was school prioritization of AODU associated with student cannabis and alcohol use behaviours. This study suggests that schools may benefit from guidance in identifying and addressing priority health concerns among their student population.