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 (Y[subscript 1]: 2012-2013) and Year 2 (Y[subscript 2]: 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 Y[subscript 1 and Y[subscript 2], 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.