Background Consideration of public preferences is desirable when making decisions on the subsidy of pharmaceuticals. Little is known about the preferences of the public for pharmaceutical funding decisions, and no study has directly compared the preferences of members of a pharmaceutical decision-making body with those of the public on whose behalf decisions are made. Objective This article reports the findings of a pilot discrete-choice experiment (DCE) undertaken to test the concept of evaluating the consistency of public and decision maker preferences for the public subsidy of pharmaceuticals. Methods A DCE was used to elicit the relative importance of gains in survival, quality of life (QOL), chance of response success and government costs in pharmaceutical funding decisions, and the impact that the initial severity of illness has on preferences. The DCE was administered to a sample of the Australian public and members of the Pharmaceutical Benefits Advisory Committee and its Economic Subcommittee. A mixed logit model was employed for analysis. Results For both samples, increased survival, QOL and chance of response success, and a reduction in cost or uncertainty (decision makers only), increased the likelihood that a pharmaceutical would be chosen for funding. Both samples were more likely to fund a pharmaceutical that was used for the treatment of severe illness. Conclusion This study sets the foundation for future research on the relative importance of decision criteria, the contexts that impact on the criteria and the extent to which funding decisions for pharmaceuticals in Australia and elsewhere are consistent with the preferences of society.