Abstract Background Emerging literature suggests accelerated weight gain in children during the pandemic; however, data from Canadian children are limited and individual factors underlying this trend remain unclear. Objectives To determine whether the COVID-19 pandemic was associated with increased yearly change in age- and sex-standardized body mass index (zBMI) in Canadian children and whether staying at home during the pandemic was associated with increased change in zBMI per year. Design/Methods A repeated-measures longitudinal study was conducted with children from an existing practice-based research network in Canada age 1-18y with at least one zBMI measurement pre- and post-onset of the pandemic. Height and weight were measured through primary care office visits and supplemented with at-home parent measurements post-pandemic. Weekly questionnaires were used to measure days stayed at home per week. Piecewise linear mixed effects models accounting for repeated measures through random effects were used to assess yearly change in zBMI. A knot location was placed at the start of the pandemic (March 14, 2020) to compare slopes pre- and post-pandemic onset. Similar mixed effects models were used to explore the association between days at home per week and change in zBMI post-pandemic onset. Stratification by sex and a sensitivity analysis in children with clinic-measured anthropometrics were explored. All models were adjusted for covariates identified a priori. Results In the overall population (n=849 children, 5070 observations), there was no significant difference in slope for yearly change in zBMI post-pandemic (Mar 2020-Sept 2022) compared to prior (Oct 2004-Mar 2020) in fully adjusted models accounting for child age, sex, maternal ethnicity, maternal BMI, family income, birthweight, breastfeeding duration, anthropometrics measurement method (clinic vs parent) and pre-COVID zBMI (post-COVID β=0.03; 95%CI -0.02,0.08; pre-COVID β=0.009; 95%CI-0.009,0.027; p-interaction=0.46). In children with clinic-measured anthropometrics (n=849, 4318 observations), there was a significant increase in yearly change in zBMI after the onset of the pandemic in the fully adjusted model (β=0.07; 95%CI 0.02,0.12) compared to prior (β=0.004; 95%CI -0.01,0.02; p-interaction=0.01). This was driven by changes in boys (post-COVID β=0.08; 95%CI 0.007,0.15; pre-COVID β=-0.003; 95%CI-0.03,0.02; p-interaction 0.04). In boys with clinic-measured anthropometrics post-pandemic onset (n=77 children, 85 observations), there was marginal evidence for increase in yearly zBMI change for every additional day at home per week in the fully adjusted model (β=0.16; 95%CI -0.006,0.32; p=0.06). Conclusion The COVID-19 pandemic was associated with accelerated increase in zBMI per year in Canadian children with clinic-measured height and weight, particularly among boys. Potential competing interests Funding was obtained by J.J. Joseph Jamnik for consultant work for Nutrigenomix Inc, a University of Toronto start-up which offers evidence-based genetic testing for personalized nutrition. Consulting work terminated July 1, 2023. This relationship is unrelated to the work submitted. Research funding: Understanding and mitigating the impacts of the COVID-19 pandemic on children, youth and families in Canada - Operating Grant. CIHR grant 468613. 2021-2024.