In 1988 Jaffe co-founded the Economics Resource Group which functioned as a consulting firm for antitrust, regulatory, and intellectual property cases.
From 1990 to 1991 Jaffe worked as a senior staff economist on the President's Council of Economic Advisers where he was responsible for antitrust, environmental, and innovation policy.
From 1994, Jaffe was on the faculty at Brandeis University in Massachusetts where he also served as the chair of the economics department from 2000 to 2002 and the Dean of Arts and Sciences from 2003 to 2011.
[2] He became Director of Motu Economic and Public Policy Research in May 2013 and was named an adjunct professor of Queensland University of Technology in early 2015.
In 2007 Jaffe received an honorable mention from the Venice Award for Intellectual Property for his work titled Innovation and its Discontents.