Infectious diarrhea is one of the many threats to the deployed military, and given limited resources, a decision to pursue a vaccine acquisition strategy should be based on best evidence that weighs costs and benefits compared to alternatives. An economic model was developed to estimate the marginal cost to avert a duty day lost due to diarrhea for a vaccine acquisition strategy compared to current clinical management, for both multiplex and pathogen-specific vaccines. Vaccines against Campylobacter and enterotoxigenic Escherichia coli appeared to be more favorable than a Shigella vaccine. This model provides an evidence-based decision tool to support prioritization in vaccine development.