This longitudinal study of children enrolled as infants in the New York State (NYS) Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) examined predictors of obesity (body mass index ≥ 95th percentile) at 3 years of age. NYS WIC administrative data which included information from parent interviews and measured heights and weights for children were used. All 50,589 children enrolled as infants in WIC between July to December 2008 and July to December 2009 and retained in WIC through age three were included. At 3 years of age, 15.1% of children were obese. Multiple logistic regression analysis showed that children of mothers who received the Full Breastfeeding Food Package when their infant was enrolled in WIC (adjusted OR = 0.52) and children with ≤2 h screen time daily at age 3 (adjusted OR = 0.88) were significantly less likely to be obese (p < 0.001) controlling for race/ethnicity, birth weight, and birthplace. In this cohort of NYS WIC participants, maternal receipt of the Full Breastfeeding Food Package (a surrogate measure of exclusive breastfeeding) is associated with lower levels of obesity in their children at age 3. The relationships between participation in WIC, exclusive breastfeeding, and obesity prevention merit further study.