This paper sets out a rationale for a new ambition of collaboration, based upon the need for new levels of investment in Africa’s research capacity. As the African Union and the European Union are developing a new strategy for jointly addressing our global challenges, they have a unique opportunity to invest in African research universities, and support new collaborative networks of universities and researchers in both continents. This is key to the ability of both continents to address our societal challenges like climate change and digital transformation. Both, the European Union and the African Union, have emphasized the importance of supporting research and innovation, and the universities within which these take place. This is a crucial time to act, to ensure that collaboration between Africa and Europe is future-oriented and strategic, and carries the support of universities, governments, and the two Unions.