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Background Food insecurity is common in Canada and impacts children more than any other age group. This study aimed to evaluate the association between participation in school food programs and food insecurity among students attending Canada’s largest urban school-based health centre program, the REACH School Network. Methods This is a cross-sectional observational study from April 2022 to June 2024 at the REACH School Network. We administered the Growth and Nutrition Questionnaire to parents of children aged 3–17 years. Questions were related to dietary intake and participation in school food programs. Our primary outcome was food insecurity, using the Hunger Vital Sign. Logistic regression estimated the association between regular school food program participation and food insecurity, adjusting for covariates. Results Of 477 eligible participants, 316 consented (66.2% response rate), and 223 were included in the analysis. The mean age was 9.21 years (SD = 3.08); 69.1% identified as male. Overall, 134 (60.1%) regularly participated in a school food program. Food insecurity was reported by 97 (43.5%) participants, with similar prevalence among participants (44.8%) and non-participants (41.6%). Logistic regression, both unadjusted (OR = 1.14; 95% CI 0.66–1.97; P  = 0.637) and adjusted (OR = 0.82; 95% CI 0.42–1.63; P  = 0.579) found no significant association between school food program participation and food insecurity. Conclusion Our study highlights the complex relationship between food insecurity and school food program participation among an at-risk, urban children. Future research is needed, with larger sample sizes and longitudinal designs to better understand these complex relationships.