ABSTRACT Background Cystic Fibrosis (CF) is a genetic life limiting disease that impacts upon quality of life. An aim of CF care is to preserve lung function, with physical activity (PA) being an important part of daily airway clearance. Ensuring children have opportunities to engage in PA at school should be an important part of their daily routine. It is important to gain parental perspectives on this, as they manage the daily care for their children. This study aims to explore parents’ perceptions of school-based PA for their children with CF. Methods Parents of children with CF (n = 10), from three regions of the UK (England, Wales and Northern Ireland) took part in online semi-structured interviews. Data were analysed using Interpretative Phenomenological Analysis (IPA). Results Although parents recognized the benefits of school-based PA for their children, systemic barriers in the school setting often inhibit daily PA for children with CF, including teachers’ misconceptions, emotional and physical barriers, and PA not being a priority. Conclusion Recommendations for practice have been developed to help engage children with CF in daily school-based PA in an inclusive way, with the hope of maintaining health outcomes for children with CF.