The objective of this study was to project the cost-effectiveness of implementing the Healthy Weight Clinic (HWC), a primary care-based intervention for 6- to 12-year-old children with overweight or obesity, at federally qualified health centers (FQHCs) nationally. We estimated intervention costs from a health care sector and societal perspective and used BMI change estimates from the HWC trial. Our microsimulation of national HWC implementation among all FQHCs from 2023 to 2032 estimated cost per child and per quality-adjusted life year (QALY) gained and projected impact on obesity prevalence by race and ethnicity. Probabilistic sensitivity analyses assessed uncertainty around estimates. National implementation is projected to reach 888,000 children over 10 years, with a mean intervention cost of $456 (95% uncertainty interval [UI]: $409-$506) per child to the health care sector and $211 (95% UI: $175-$251) to families (e.g., time participating). Assuming effect maintenance, national implementation could result in 2070 (95% UI: 859-3220) QALYs gained and save $14.6 million (95% UI: $5.6-$23.5 million) in health care costs over 10 years, yielding a net cost of $278,000 (95% CI: $177,000-$679,000) per QALY gained. We project greater reductions in obesity prevalence among Hispanic/Latino and Black versus White populations. The HWC is relatively low-cost per child and projected to reduce obesity disparities if implemented nationally in FQHCs.