Background In the context of limited health care budgets in countries where Neglected Tropical Diseases (NTDs) are endemic, scaling up disease control interventions entails the setting of priorities. However, solutions based solely on cost‐effectiveness analyses may lead to biased and insufficiently justified priorities. Objectives The objectives of this paper are to 1) demonstrate how a range of equity concerns can be used to identify feasible priority setting criteria, 2) show how these criteria can be fed into a multi‐criteria decision‐making matrix, and 3) discuss the conditions under which this decision‐making procedure should be carried out in a real‐world decision‐making context. Methods This paper draws on elements from theories of decision analysis and ethical theories of fair resource allocation. We explore six typical NTD interventions by employing a modified multi‐criteria decision analysis model with predefined criteria, drawn from a priority setting guide under development by the WHO. To identify relevant evidence for the six chosen interventions, we searched the PubMed and Cochrane databases. Discussion Our in vitro multi‐criteria decision analysis suggested that case management for visceral leishmaniasis should be given a higher priority than mass campaigns to prevent soil‐transmitted helminthic infections. This seems to contradict current health care priorities and recommendations in the literature. We also consider procedural conditions that should be met in a contextualised decision‐making process and we stress the limitations of this study exercise. Conclusion By exploring how several criteria relevant to the multi‐facetted characteristics of NTDs can be taken into account simultaneously, we are able to suggest how improved priority settings among NTDs can be realised.