Obesity is a serious problem among children in Mexico. In 2010, the government implemented a national food and physical activity policy in elementary schools, to prevent obesity. The goal of this study is to assess the implementation of this policy, using the logic model from a descriptive survey with national representativeness at the elementary school level and based on a stratified cluster design. We used a systematic random sampling of schools (n = 122), stratified into public and private. We administered questionnaires to 116 principals, 165 members of the Food and Physical Activity Committees, 132 food school food vendors, 119 teachers, 348 parents. This study evidences a significant deviation in implementation from what had been planned. Our lessons learned are the importance to: base the design/implementation of the policy on a theoretical framework, make programs appealing to stakeholders, select concrete and measurable objective or goals, and support stakeholders during the implementation process.