The H5N1 influenza threat is resulting in global preparations for the next influenza pandemic. Pandemic influenza planners are prioritizing scarce vaccine, antivirals, and public health support for different segments of society. The freight, bulk goods, and energy transportation network comprise the maritime, rail, air, and trucking industries. It relies on small numbers of specialized workers who cannot be rapidly replaced if lost due to death, illness, or voluntary absenteeism. Because transportation networks link economies, provide critical infrastructures with working material, and supply citizens with necessary commodities, disrupted transportation systems can lead to cascading failures in social and economic systems. However, some pandemic influenza plans have assigned transportation workers a low priority for public health support, vaccine, and antivirals. The science of Transportation Geography demonstrates that transportation networks and workers are concentrated at, or funnel through, a small number of chokepoints and corridors. Chokepoints should be used to rapidly and efficiently vaccinate and prophylax the transportation worker cohort and to implement transmission prevention measures and thereby protect the ability to move goods. Nations, states, the transportation industry and unions, businesses, and other stakeholders must plan, resource, and exercise, and then conduct a transportation health assurance and security campaign for an influenza pandemic.