In recent years, challenges such as international terrorism, transnational organized crime and illegal immigration have rendered mobility and border security top priorities and issues for cooperation among international actors. This article looks specifically at mobility and related border concerns as key topics in relations between the European Union and Azerbaijan. Azerbaijan has become a crucial ally for the European Union for multiple reasons. First, it is located in a strategic position, at the crossroads between East and West; second, it has recently become a key actor in the energy game, proposing itself as an alternative and reliable source of energy; third, it is member of the Eastern Neighborhood, where regional stability has direct bearing upon the EU’s security. By outlining the ways in which these challenges may also be potentially disruptive for Azerbaijan’s national interests and overall security, the article considers the extent of existing cooperation on mobility and border security, up until the recent signature of the Mobility Partnership (2013). While relations have rapidly expanded over recent years, the article concludes that without a clear regional vision of the EU or proper coordination on these transborder issues, further development will be impeded.