BACKGROUND Despite the importance of breakfast consumption, breakfast skipping is common among Canadian youth. This study examines how changes to school‐based breakfast programs are associated with breakfast‐skipping behavior. METHODS Using school‐level longitudinal data from Year 1 (Y1: 2012‐2013) and Year 2 (Y2: 2013‐2014) of the COMPASS study, quasi‐experimental methods evaluated the impact over time that changes to school‐based breakfast programs had on breakfast skipping or participating in school‐based breakfast program. RESULTS Between Y1 and Y2, the school‐level prevalence of breakfast skipping (54.5%‐54.9%) and breakfast program participation (12.3%‐13.6%) increased. Of the 43 participating schools, 5 implemented a new school breakfast program. Among the intervention schools, 1 school (School 4) observed a significant, and 1 school (School 3) observed a significant increase in the school‐level prevalence of skipping breakfast; there was no significant change in the other 3 intervention schools. CONCLUSIONS Despite the availability of free school breakfast programs, the majority of youth skipped breakfast at least once a school week. Owing to the variation in the types of programs implemented, additional evaluation evidence is necessary to determine which students benefited the most from these programs.