Hendra virus (HeV), a potentially fatal zoonotic disease spread by flying foxes, to date has always infected humans via a spillover event from equine HeV infection. In a theoretical case study, we compared the impacts of two different HeV prevention strategies – vaccination and flying fox roost removal – using a recently developed framework that considers different stakeholder group perspectives. The perspectives of the four selected stakeholder groups regarding intangibles were inferred from public discussions and coverage in the media. For all stakeholder groups, the option to vaccinate horses was found to add value to the economic results when the intangible impacts were included in the analysis, while the option for roost removal unanimously detracted from economic analysis value when the intangible impacts were included. Both the mean and median stakeholder-adjusted value ratios (2.25 and 2.12, respectively) for vaccination were inflated when intangible impacts were included, by value-adding to the results of a traditional economic analysis. In the roost removal strategy, these ratios (1.19 and 1.16, respectively) were deflated when intangible impacts were included. Results of this theoretical study suggest that the inclusion of intangible impacts promotes the value of a two-dose initial vaccination protocol using a subunit vaccination considered to offer complete protection for horses, as a strategy to control HeV, whereas roost removal becomes an even more costly strategy. Outcome of the analysis is particularly sensitive to the intangible value placed on human health. Further evaluation – via sociological methods – of values placed on intangibles by various stakeholder groups is warranted.