Born in Nantes in Brittany, France, Dauphas received a B.Sc. degree from  in 1998. The same year, he obtained an M.Sc. from , at the National Polytechnic Institute of Lorraine (; INPL). In 2002, also from INPL, he was awarded a Ph.D. in geochemistry and cosmochemistry, working with Bernard Marty and Laurie Reisberg. He then completed his postdoctoral research at the Enrico Fermi Institute of the University of Chicago and the Field Museum of Natural History from 2002 to 2004, before joining the faculty at the University of Chicago in 2004.