 Werner was a research officer at the CNRS (National Center of Scientific Research, Centre national de la recherche scientifique) from 1991 to 1997, during which period he held a two-year Leibniz Fellowship, at the University of Cambridge.He has been Professor at
the University of Paris-Sud in Orsay from 1997 to 2013 (and has also been lecturing at the École Normale Supérieure from 2005 to 2013).Werner has received several awards, including the Rollo Davidson Prize in 1998, the Prix Paul Doistau–Émile Blutet in 1999, the Fermat Prize in 2001, the Grand Prix Jacques Herbrand of the French Academy of Sciences in 2003, the Loève Prize in 2005, the 2006 SIAM George Pólya Prize with his collaborators Gregory Lawler and Oded Schramm or the Heinz Gumin Prize () in 2016.