In South Korea, free lunch programs have been employed nationwide since 2008. This study investigated the effect of free school lunch program participation on the dietary intakes of South Korean children. We conducted a multi-period cross-sectional study of 2,808 children (age range, 7-12 years) at elementary schools in all 16 regions of South Korea. Our estimated results indicate that the program led to reduced nutritional intakes of the lower grade students (7-9 years). Considering overindulgence in sodium, reduced intakes of sodium is positive effect. However reduced intakes of fat and arbohydrate could be trouble for students. On the other hand, no effect was found for the upper grades after implementing free lunch programs. Accordingly, we found that simply providing free school lunches to students without considering the balanced intake of key dietary components may not be the ideal approach to achieving health improvements in children.