The 'Be Active Stay Healthy' (BASH) health-related exercise (HRE) programme was delivered to Year 5 students (age 9-10 years) in two primary schools situated in the same area of a northwest England town. BASH aims to improve students' participation in and knowledge of HRE through structured physical activities. Fifty-five students completed pre- and post-programme HRE knowledge and understanding questionnaires. Moderate to vigorous physical activity (MVPA) levels of 13 students were assessed using accelerometers during two contrasting lessons focusing on optimal activity levels (active) and cognitive learning (cognitive). Mean percentage of correct questionnaire answers improved from 60.8 to 83.8% (P = 0.0001, effect size (ES) = 1.44), and questionnaire performance was significantly better among students in one of the schools (P = 0.017, ES = 0.72). Boys engaged in MVPA for 11% more time than girls during the active lessons (P = 0.0006, ES = 1.21) but MVPA during cognitive lessons was similar. The BASH programme has potential to use structured physical activity as a medium to enhance students' HRE knowledge, particularly in relation to the fundamental understanding of healthy and active lifestyles. HRE knowledge may differ between schools, even when they are similarly sized and located, with analogous student catchment areas. Recommendations for the future delivery and evaluation of the programme are made.