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Objectives. To examine individual-, school-, and neighborhood-level factors associated with COVID-19 primary and booster vaccination among New York City public school students. Methods. We analyzed data from a population-based cohort study of 917 062 students aged 5 to 18 years enrolled in 2021/2022. Enrollment data were linked to the Citywide Immunization Registry, Medicaid claims, and neighborhood indicators (January 2020-July 2023). We assessed multivariable regression associations between vaccination status and demographic, clinical, school, and contextual characteristics. Results. Overall, 51.3% of all students completed the primary series and 10.8% received a booster. Uptake was highest among non-Hispanic Asian students (72.1%; 95% confidence interval [CI] = 71.9, 72.3) and lowest among non-Hispanic Black (42.2%; 95% CI = 42.0, 42.4) and non-Hispanic White students outside Manhattan (39.7%; 95% CI = 39.5, 40.0). Students with preexisting conditions were modestly more likely to have received vaccination than peers (54.9%; 95% CI = 54.8, 55.1 vs 49.8%; 95% CI = 49.7, 49.9). Uptake increased with older age and proximity to vaccination sites but was lower among Medicaid-enrolled students. Conclusions. Coverage in the largest US school district was lower than national pediatric estimates, with only modestly higher coverage among children at elevated medical risk, despite their prioritization in vaccination efforts. Public Health Implications. Children at elevated medical risk remained undervaccinated. Addressing barriers in insurance, neighborhood, and care delivery systems is critical to improving vaccine uptake. (Am J Public Health. Published online ahead of print August 6, 2026:e1-e11. https://doi.org/10.2105/AJPH.2026.308604).