Abstract Background Public health strategies that focus on legislative and policy change involving chronic disease risk factors such as unhealthy diet and physical inactivity have the potential to prevent chronic diseases and improve quality of life as a whole. However, many public health policies introduced as part of public health reform have not yet been analyzed, such as in British Columbia and Ontario. The purpose of this paper is to present the results of a descriptive, comparative analysis of public health policies related to the Healthy Living Core Program in British Columbia and Chronic Disease Prevention Standard in Ontario that are intended to prevent a range of chronic diseases by promoting healthy eating and physical activity, among other things. Methods Policy documents were found through Internet search engines and Ministry websites, at the guidance of policy experts. These included government documents as well as documents from non-governmental organizations that were implementing policies and programs at a provincial level. Documents (n = 31) were then analysed using thematic content analysis to classify, describe and compare policies in a systematic fashion, using the software NVivo. Results Three main categories emerged from the analysis of documents: 1) goals for chronic disease prevention in British Columbia and Ontario, 2) components of chronic disease prevention policies, and 3) expected outputs of chronic disease prevention interventions. Although there were many similarities between the two provinces, they differed somewhat in terms of their approach to issues such as evidence, equity, and policy components. Some expected outputs were adoption of healthy behaviours, use of information, healthy environments and increased public awareness. Conclusions The two provincial policies present different approaches to support the implementation of related programs. Differences may be related to contextual factors such as program delivery structures and different philosophical approaches underlying the two frameworks. These differences and possible explanations for them are important to understand because they serve to contextualize the differences in health outcomes across the two provinces that might eventually be observed. This analysis informs future public health policy directions as the two provinces can learn from each other.