This paper estimates the cost-effectiveness of a 20% price discount on healthy food and beverages with and without consumer nutrition education, as trialled in remote Northern Australia. Changes in actual store sales, from the pre-discount baseline period, were analysed for population impact on consumption of fruit and vegetables, water and artificially sweetened soft drinks, in addition with total dietary weight (grams), energy (Mega Joules), and sodium (milligrams). Disability Adjusted Life Years (DALYs), arising from changes in dietary risk factor prevalence in the population, were estimated as the primary health outcome in a multi health-state Markov model. The costs of the strategies were sourced from paid invoices and time estimates of staff providing store-based discount promotion and consumer education. The incremental cost-effectiveness ratio adopted a partial societal perspective, (including health and retail sector costs), as cost per DALY averted and was presented in 2011 Australian dollars. The price discount, helped address a gap in food price equity for residents of remote communities. However, the discount strategy, with or without consumer education led to a net loss of population health -36 95%CI (-47,-25) or -21(-28, -15) DALYs respectively, at increased cost to the retail and health sectors, of AUD860000 95%CI (710000, 1million) or AUD500000 (410000, 590000). The strategies trialled were thereby categorised as dominated by current practice while acknowledging considerable uncertainty surrounding the health outcome estimates. The 20% discount on limited targeted products appeared to need to be considered in conjunction with other marketing strategies to support healthy food choices, if remote Australian Indigenous population health is to be improved.