Whole-of-school programmes (WSPs) are recommended to promote physical activity for adolescents. The Active School Flag (ASF) programme for secondary-level schools is one such WSP. Due to the difficulties of incorporating WSPs into the complex school system, there is a risk of poor implementation. The monitoring of unanticipated influences can help to understand key implementation processes prior to scale-up. The aims of this study were to identify perceived facilitators and barriers to implementing the ASF and recommend evidence-based implementation strategies. Focus groups and interviews (N = 50) were conducted in three schools with stakeholders involved in programme implementation, i.e. school management (n = 5), ASF coordinator (n = 4), student-leaders (aged 15-16 years) (n = 64) and staff committee (n = 25). Transcripts were analysed using codebook thematic analysis and were guided by the Consolidated Framework for Implementation Research. Implementation strategies were identified and were selected systematically to address contextual needs. Three themes surrounding the facilitators and barriers to implementation were generated: intervention design factors (e.g. capacity building and knowledge of implementers; and interest and buy-in for the programme), organizational factors (e.g. optimization of people and the busy school environment) and interpersonal factors (e.g. communication and collaboration). The examination of facilitators and barriers to implementation of the ASF has assisted with the identification of implementation strategies including (not limited to) a shared leadership programme for student leaders and a more flexible timeline for completion. These facilitative implementation strategies may assist in the effective implementation of the ASF.