Lionel Fontagné holds a degree from the University of Paris (Agrégé des Universités, 1990), is an adviser to the Directorate for the Economy and International Cooperation of the Banque de France and is on secondment from the University of Paris I Panthéon-Sorbonne and the Paris School of Economics. He directed the Centre for Prospective Studies and International Information (CEPII) from 2000 to 2006.

He is also a scientific advisor at CEPII (Paris) and a research fellow at CESifo (Munich).

He was a member of the Economic Analysis Council (CAE) from 2001 to 2010, from 2012 to 2016, he was Director of the Sorbonne Economics Centre (UMR 8174 of the CNRS), from 2014 to 2018, he was a part-time Professor at the European University Institute of Florence and has worked as a substitute Professor at the Free University of Brussels and Professor at the University of Nantes. He has also worked as a consultant to the Bank of France, the International Trade Centre (UNCTAD-WTO, Geneva), the Development Centre of the OECD, the OECD Directorate for Industry, Science and Technology, the World Bank and the French and Luxembourg Ministries of Finance.

He has written numerous studies on international trade issues, trade policy and trade and the environment, and in 1999, he was awarded the Open Economies Review prize for best article for his contribution to the debate on optimal currency areas. In 2008, he received an Emerald Management Reviews citation of excellence for his contribution to understanding the impact of competition from emerging countries. In 2007, and again in 2018, he received the distinction of Research Fellow from the Global Trade Analysis Project (GTAP, Purdue University). In 2023, he joined the GTAP Research Fellow Hall of Fame in recognition of his contributions to trade policy analysis.