This study was informed by the body of literature on pupil knowledge and its potential contributions to developing healthy and active lifestyles, along with the focus of various current national physical education standards on cognitive outcomes. This study aimed to investigate the impact of conceptual-based intervention programmes in two rural schools on pupils' healthy behaviour knowledge. Schools used a similar intervention model of healthy behaviour concepts taught as part of physical education classes, by classroom teachers, and in wellness week activities. The intervention in both schools was based on the Fitness for Life curricular model (i.e. materials for classroom teachers and for physical education teachers). Pupil healthy behaviour knowledge was tracked over time to determine the impact of the intervention programmes. Analysis of variance (ANOVA) was used to compare average percentage of correct responses within school, across time within a year, and across years. ANOVA results showed a significant main effect for grade (F(5, 1152) = 33.10, p < 0.0001, n[superscript 2] = 0.125), school (F(1, 1152) = 75.23, p < 0.0001, n[superscript 2] = 0.061), time (F(1, 1152) = 164.71, p < 0.0001, n[superscript 2] = 0.125), and year (F(1, 1152) = 6.27, p = 0.012, n[superscript 2] = 0.005), and a significant three-way interaction among grade, time, and year (F(13, 1152) = 6.76, p < 0.0001, n[superscript 2] = 0.07). The findings of this study suggest that pupils can acquire healthy behaviour knowledge using several different intervention points of instruction, particularly in rural areas. This study also highlights the need to help pupils in these settings improve their healthy behaviour content knowledge.