Physical activity and obesity counselling have both been gaining increasing interest in preventive health and treatment. However, most healthcare professionals do not provide advice on these topics nearly as often as they should. There are many reasons for this. Common barriers for the provision of brief advice on physical activity and obesity in both primary and secondary care are lack of time, motivation and knowledge. Systematic reviews have been published on the barriers of physical activity and obesity counselling in the primary care setting, but there is no published work on the barriers present in secondary care. This systematic review aims to assess all published data that discuss the barriers of physical activity and obesity counselling as noted by healthcare providers in secondary care. Four databases will be searched using the same search strategy, and the findings will be compiled using the COM-B model to explore the frequency of a reported barrier. This systematic review will be beneficial not only to practicing healthcare providers, but also the educational and managerial staff of secondary care facilities, as it may highlight the need for further training to fill gaps in the provision of preventive healthcare.