From 1999 to 2004, Jeffery was professor of politics at the University of Birmingham. In 2004, he was appointed professor of politics at school of social and political studies, University of Edinburgh. From 2009 to 2012, he became head of school of social and political studies. In 2012, he was appointed vice principal of public policy and in 2014 as senior vice principal of the University of Edinburgh. In 2019, he joined University of York as vice chancellor and president.