Berlin University Alliance is a University Consortium of Excellence funded by the Federal Ministry of Education and Research (BMFTR) and the State of Berlin as part of the federal and state excellence strategy. The four partners of Berlin University Alliance - Freie Universität Berlin, Humboldt-Universität zu Berlin, Technische Universität Berlin, and Charité - Universitätsmedizin Berlin - were the first University Consortium of Excellence in Germany to receive funding with their application “Crossing Boundaries toward an Integrated Research Environment.” Funding began on November 1, 2019. On March 11, 2026, the Excellence Commission, consisting of the federal and state ministers of science and internationally renowned figures from science and university management, decided to continue funding Berlin University Alliance as a University Consortium of Excellence with the application "Beyond Boundaries: A Joint Agenda for Berlin as an Open Knowledge and Innovation Space" for another seven years (2027-2033).

A prerequisite for continued funding as University Consortium of Excellence was success in the “Clusters of Excellence” funding line of the Excellence Strategy research competition. On May 22, 2025, the Berlin University Alliance partners received notification of funding for five clusters of excellence. The interdisciplinary research projects have been funded since 2026 for an initial period of seven years. An extension of the funding for a further seven years is possible on the basis of a continuation application.