Jorgensen earned a bachelors degree from Princeton University in 1970 and a Ph.D. from Harvard University in 1975 in Chemical Physics while studying under Elias J. Corey. Jorgensen then worked at Purdue University from 1975 to 1990 first as an assistant professor and then later as a Professor. He joined the Yale faculty in 1990 and has remained there since. Jorgensens work has been recognized by many awards including election to the American Academy of Arts and Sciences, the National Academy of Sciences, and the International Academy of Quantum and Molecular Sciences. He has also received the ACS Award for Computers in Chemical and Pharmaceutical Research, the ACS Hildebrand Award, the Tetrahedron Prize, and Arthur C. Cope Award.