The European Universities Initiative (EUI) promotes European values and identity and aims to revolutionise the quality and competitiveness of European Higher Education. As part of this effort, the University Network for Innovation, Technology and Engineering (Unite!) is working on developing a Joint Program (JP) offer with embedded mobility and flexibility. To achieve this goal, we present in this paper the major challenges in implementing Flexible Study Pathways (FSP) at a transnational level identified in a survey conducted at the seven partner Universities of Unite!. The most desirable forms of flexibility regarding content of course/program were Elective Courses outside the domain and inside the degree of specialisation. Main difficulties identified by partners are related to academic calendars, time cost to organise FSP, legal matters, program agendas and ensuring the achievement of learning outcomes. The results of this analysis show possible directions for the development of a European degree, which will require effective communication and stakeholder coordination and engagement.