Bagger's research deals with high-energy physics, supersymmetry, and string theory. He was at Princeton's Institute for Advanced Study for the academic year 1985–1986 and in 1998. He was elected in 1997 a Fellow of the American Physical Society and in 2008 a Fellow of the American Association for the Advancement of Science. He was an associate editor of Physical Review Letters from 1990 to 1993 and of Physical Review D from 1998 to 2007. He joined in 1997 the editorial board of the Journal of High Energy Physics and in 1998 the editorial board of Physics Reports.