Research and innovation is one of Flanders’ priorities and over the last three decades its public funding has strongly increased. Universities are key actors in this strategy. They have a large autonomy and receive a substantial share of additional R&D expenditures as lump sum funding.The Flemish authorities use quantitative indicators to allocate these lump sums to the universities. The funding formulae take into account each institution’s size, its research performance and, if relevant, its valorization activities. Also significant is the realization of governmental priorities, such as mobility and diversity of the academic staff. This paper describes the development of the Flemish university funding model, analyses its weaknesses and its strengths, and compares it with nine national metrics-based research performance funding systems.Policy highlightsFlanders, like many other regions and nations, has adopted performance-based research funding systems (PRFSs) to improve and provide accountability for its science and innovation system. The Flemish PRFS criteria have evolved considerably over the last three decades, and due to competition between universities and a consensus model of political decision making, the funding formula is comparatively complex.Building on an historical background of lump sum payments to universities, supporting both education and research, special supplementary funds for blue-sky research (BOF) and for strategic applied research, innovation, and outreach activities (IOF) were introduced by the Flemish government in 1994 and 2004, respectively. The “three-legged stool” funding mechanism for research in Flanders is unique within Europe.The introduction of publication and citation metrics in 2003 changed the character of the Flemish PRFS considerably, previously focused on measures of a university’s size in terms of students, degrees granted, and previous funding. Humanities and social sciences (HSS) research metrics were considered only after first adoption of bibliometric methods ...