IntroductionNorthern communities in Canada experience a disproportionate burden of chronic diseases including mental illness. To mitigate the growing health inequalities, an ongoing Comprehensive School Health program promoting healthy lifestyle behaviours and mental health and well-being was expanded to rural and remote northern communities. We report on the program’s impact on knowledge, attitudes, lifestyle behaviours (healthy eating, physical activity, screen time), weight status and the mental health and well-being of elementary school students during the first four years of implementation. MethodsFollowing a repeated cross-sectional design, we surveyed 440, 352 and 384 Grade 4 to 6 students (9–12 years old) from eight schools in 2016, 2018 and 2020/21, respectively. Students were approximately equally represented by girls and boys. ResultsBetween 2016 and 2018, students reported modest increases in vegetable and fruit consumption and dietary variety; declines in screen time; no changes in physical activity; and declines in attitudes toward healthy lifestyle and in mental health and well-being. Between 2018 and 2020/21, lifestyle behaviours deteriorated substantially, while attitudes and mental health and well-being continued to decline. ConclusionA program that was successful in socioeconomically disadvantaged urban neighbourhoods had a favourable, though modest, impact on selected lifestyle behaviours, but not on attitudes and mental health and well-being, in rural and remote northern communities. In light of cultural differences and logistical challenges in Canada’s North, systematic and proactive adaptations to local contexts, increased intensity, and longer program delivery are essential to facilitate sustainable improvements in lifestyle behaviours and mental health and well-being.