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Background  The development of public health policy is inextricably linked with governance structure. In our increasingly globalized world, human migration and infectious diseases often span multiple administrative jurisdictions that might have different systems of government and divergent management objectives. However, few studies have considered how the allocation of regulatory authority among jurisdictions can affect disease management outcomes.    Methods  Here we evaluate the relative merits of decentralized and centralized management by developing and numerically analyzing a two-jurisdiction  SIRS  model that explicitly incorporates migration. In our model, managers choose between vaccination, isolation, medication, border closure, and a travel ban on infected individuals while aiming to minimize either the number of cases or the number of deaths.    Results  We consider a variety of scenarios and show how optimal strategies differ for decentralized and centralized management levels. We demonstrate that policies formed in the best interest of individual jurisdictions may not achieve global objectives, and identify situations where locally applied interventions can lead to an overall increase in the numbers of cases and deaths.    Conclusions  Our approach underscores the importance of tailoring disease management plans to existing regulatory structures as part of an evidence-based decision framework. Most importantly, we demonstrate that there needs to be a greater consideration of the degree to which governance structure impacts disease outcomes.    Supplementary Information  The online version contains supplementary material available at (10.1186/s12889-021-11797-3).

Governance structure affects transboundary disease management under alternative objectives