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The COVID-19 pandemic presents an interesting case study to examine the distribution between internal and external competences within the Federal Republic of Germany about border policies. On the one hand, health policies–which are in Germany mainly a competence of the Länder–and their impact on internal borders have to be considered. On the other hand, there are also external border policies of Germany–which are mainly a competence of the Bund–and which have an impact on the neighboring States if a process of (re)bordering takes place. Finally, one must consider how the border polices insert themselves into the framework the European Union and its competences for border management. This paper retraces how the system of German cooperative federalism has first revealed itself as an obstacle to a coordinated management of the crisis leading to an internal bordering between Länder, and how it then evolved towards a re-equilibrium of competences between the Bund and the Länder concerning health policies. It then shows that, facing the process of external bordering, German cooperative federalism has become an asset for a better cross-border cooperation during the pandemic. It further demonstrates that the EU has become an important actor to favor a European coordination of health and border policies.