Background: There is little evidence of whether or not those who have attended cardiac rehabilitation (CR) are meeting the physical activity guidelines recommended for secondary prevention of cardiovascular disease. In healthy individuals, there is evidence, that even if individuals are meeting the physical activity guidelines, the harmfulness of too much sedentary behaviour remains (active couch potato (ACP) phenomenon). Currently, there appears to be no evidence of the ACP phenomenon in those attending CR. The aims of the study are to examine the level of physical activity and sedentary behaviour in those with coronary heart disease (CHD) who have attended CR, and to investigate the potential independent associations between these behaviours and cardio-metabolic health, health-related quality of life, exercise capacity, anxiety and depression. Methods: A prospective cohort study will be conducted in Australia over 12-months. Baseline data from this study will contribute to an international, multi-centre cross-sectional study (Australia, New Zealand, United States of America, South Africa, Spain, and Portugal). Adults currently enrolled in a 6-week phase II cardiac rehabilitation program with stable CHD and receiving optimal medical treatment +/- revascularisation will be recruited. Outcome measures will be taken at baseline (commence CR), 6 weeks (complete CR), 6 and 12-months. Physical activity and sedentary behaviour will be measured using accelerometry and two questionnaires (Active Australia Survey, Past-Day Adults' Sedentary Time questionnaire). Health outcomes will include body mass index, waist-to-hip ratio, lipid profile, blood glucose level, quality-of-life (MacNew), exercise capacity (6-min walk test), anxiety and depression (Hospital Anxiety and Depression Scale). Discussion: There has been limited investigation of the physical activity levels and sedentary behaviour of individuals with CHD attending CR. There are no studies assessing the relationship of these behaviours with health outcomes over the short and medium-term. As in healthy individuals, physical activity and sedentary behaviour may have independent effects on cardiovascular risk factors in people with CHD, which may contribute to recurrent cardiovascular events. If this is so, reducing sedentary behaviour may be a feasible first-line, additional and more achievable strategy to improve the health of those with CHD, alongside traditional recommendations to increase the time spent in moderate-to-vigorous intensity physical activity. Trial registration: Australian New Zealand Clinical Trials Registry (ANZCTR): ACTRN12615000995572.