Food insecurity remains a persistent public health problem for children in the U.S. and is thought to have consequences for child physical, social and academic development. The School Breakfast Program, the National School Lunch Program, and Supplemental Food and Nutrition Program for Women, Infants and Children (WIC) are federally funded programs intended to avert food insecurity and its consequences for children. These nutrition programs have also been associated with child physical, social and academic developmental outcomes. Further research is needed to investigate the complex relations between variables and to establish greater plausibility that associations are causal in nature. This study investigated the causal effects of household food insecurity and child nutrition program participation by using longitudinal data and statistical methods to account for potential bias. Fixed-effects modeling was utilized to minimize bias resulting from selection to participate and to take advantage of dynamic changes in household food insecurity status and program participation between kindergarten and 3rd grade. Household food insecurity, independent of household income and other child- and household-level factors, was associated with poorer social skills and reading performance development among girls, and with greater weight gain among boys. National School Lunch Program participation was associated with better mathematics and reading performance for children. The effects of National School Lunch Program participation were stronger for children with greater socioeconomic need compared to those with less socioeconomic need, suggesting that food assistance participation may impact child development by modifying the effects of stress-related hardships. Neither school breakfast participation nor school lunch participation was associated with greater weight gain. In conclusion, food insecurity may exert its detrimental effects through nutritional and non-nutritional (i.e., stress-related) mechanisms. Similarly, school nutrition programs may protect children against the effects of food insecurity through nutritional and non-nutritional mechanisms. Further research into potential mechanisms underlying these associations is warranted. Policy implications of the findings are discussed.