Bagger received his bachelor's degree in 1977 from Dartmouth College. He spent the academic year 1977–1978 at the University of Cambridge as a Churchill Scholar. In 1978 he became a graduate student in physics at Princeton University, where he received his PhD in 1983. His doctoral thesis Matter Couplings in Supergravity Theories was supervised by Edward Witten. He was a postdoc from 1983 to 1986 at the Stanford Linear Accelerator Center. He was from 1986 to 1989 an associate professor at Harvard University. At Johns Hopkins University he became in 1989 a full professor, holding a professorial chair there until 2014. In 2014 he was appointed director of TRIUMF, Canada's national laboratory for particle and nuclear physics.