Background Childhood obesity is a recognised public health problem and around 25% of Australian children are overweight or obese. A major contributor is the obesogenic environment which encourages over consumption of energy dense nutrient poor food. Taxation is commonly proposed as a mechanism to reduce consumption of poor food choices and hence reduce rates of obesity and overweight in the community. Methods/Design An economic model will be developed to assess the lifetime benefits and costs to a cohort of Australian children by reducing energy dense nutrient poor food consumption through taxation mechanisms. The model inputs will be derived from a series of smaller studies. Food options for taxation will be derived from literature and expert opinion, the acceptability and impact of price changes will be explored through a Citizen's Jury and a discrete choice experiment and price elasticities will be derived from the discrete choice experiment and consumption data. Discussion The health care costs of managing rising levels of obesity are a challenge for all governments. This study will provide a unique contribution to the international knowledge base by engaging a variety of robust research techniques, with a multidisciplinary focus and be responsive to consumers from diverse socio-economic backgrounds.