Objectives. To assess multilevel factors associated with variation in COVID-19 vaccination rates in a US network of community health centers. Methods. Using multilevel logistic regression with electronic health record data from ADVANCE (Accelerating Data Value Across a National Community Health Center Network; January 1, 2022-December 31, 2022), we assessed associations between health care delivery site-level (n = 1219) and patient-level (n = 1 864 007) characteristics and COVID-19 primary vaccine series uptake. Results. A total of 1 337 440 patients completed the COVID-19 primary vaccine series. Health care delivery site characteristics were significantly associated with lower series completion rates, including being located in non-Medicaid expansion states and isolated or rural communities and serving fewer patients. Patient characteristics associated with significantly lower likelihood of completing the vaccine series included being Black/African American or American Indian/Alaska Native (vs White), younger age, lower income, being uninsured or publicly insured (vs using private insurance), and having fewer visits. Conclusions. Both health care delivery site- and patient-level factors were significantly associated with lower COVID-19 vaccine uptake. Community health centers have been a critical resource for vaccination during the pandemic. (Am J Public Health. 2024;114(11):1242-1251. https://doi.org/10.2105/AJPH.2024.307773).