Nowotny is one of the founding members of the European Research Council, which has been established to fund frontier research at EU level based on the sole criteria of scientific excellence and pan-European competition. There she served as the Vice President and in February 2010, Nowotny was unanimously elected to the position of President of the European Research Council after the resignation of the founding president, Fotis Kafatos. As president of the ERC, she promoted increases in research funding across Europe, and advised new EU member states to increase funding support for their own research programs to prevent a "brain drain". She held the position until December 2013.