Schools have the potential to positively impact on population health. Food and physical activity practices at Irish post-primary schools are not currently subject to national policy. The aim of this study was to carry out a cross-sectional study with students and staff from Irish post-primary schools (male, female, mixed gender, urban, rural, disadvantaged) to explore the effect of the school setting on the dietary and physical activity behaviours of students. A mixed methods approach was used, incorporating participatory methods with students where possible. Peer-led focus groups and visual techniques were conducted. Principals and teachers were interviewed. Quantitative measures with students included anthropometry, fitness testing, and 4-day food and activity diaries. A total of 393 students from fourth-year classes (15-17 year olds) took part. Overweight and obesity prevalence in the sample was 20%, with higher abdominal obesity observed among girls. Self-reported physical activity level was the strongest predictor of fitness. 55.4% of girls and 44.8% of boys reported low physical activity levels. Significant differences in energy and nutrient intakes were observed between home prepared, and school and externally purchased lunches, with the latter two sources being less healthy than home. Factors influencing unhealthy food choice during school included independent school food operators, an open lunch time campus, close proximity to shops, price, taste, convenience, marketing, and peer norms. Gender differences in school physical activity cultures were observed, with boys having more access to social supports and facilities for activity outside of PE compared to girls. The physical environments of the schools, as depicted by students through photos indicated that school buildings, facilities and grounds are inadequate to support current healthy eating and physical activity recommendations for young people. Students demonstrated their agency to become involved in research about health promotion issues within their schools. These findings have implications for policy makers as they highlight multi-level factors that could be addressed by local and national policy for the benefit of young people’s health.