Background Increasing concern about adolescent mental health problems has resulted in schools being identified as central sites for their prevention (PsycInfo; ERIC 2000–2012). In this context, SEAL for secondary schools was launched in 2007. Method The implementation strand of the national evaluation of secondary SEAL comprised longitudinal case studies of nine schools and used multiple methods and data sources, including interviews, observations and document review. Results Implementation was variable, both within and between schools; barriers were identified at programme, teacher and school levels. Conclusions Implementation issues identified have implications for SEAL and school‐based mental health prevention and promotion interventions more generally.