This study sought to understand the current challenges mainstream secondary schools in England face in creating a health promoting school culture for diet and physical activity behaviours. An in-depth qualitative case study of two purposely selected state-funded schools, including interviews with teachers, observations of school activities including meal breaks and a qualitative survey with parents was done. Inductive thematic analysis was used to explore emerging themes. Additional interviews with the leadership team from four further schools were used to develop and refine emerging themes. Four main themes emerged from the data: competing pressures, school environment, personnel and policy. Results demonstrate that schools recognize they have role to play in promoting healthy lifestyle behaviours to pupils; however, several significant barriers were identified such as lack of government support and regulation, school structures and organization, focus on core subjects, business-run canteens and lack of family and community engagement. Given the importance of maintaining a healthy weight throughout the life course, schools have an important role to play in creating healthy environments in which students can easily make a healthy choice. Future school promotion initiatives need to consider addressing the barriers that schools face by working with them and the communities in which they are embedded.