Born in the United Kingdom, Rathjen moved to South Australia in 1965 when he was a child. He was educated at Blackwood High School in Adelaide. He studied Science at the University of Adelaide, majoring in biochemistry and genetics, and completing an honours degree. Rathjen was awarded a Rhodes Scholarship to New College, Oxford in 1985 where he continued research into certain plant pathogens called viroids and their association with RNA behaviour. He was awarded a DPhil in 1987, and then worked as a postdoctoral researcher on embryonic stem cells from 1988 to 1990. Rathjen returned to the University of Adelaide, where he worked as Lecturer in Biochemistry from 1990 to 1995 and Professor in Biochemistry from 1995 to 2006. He was appointed to the Chair of Biochemistry in 1995. He became Head of the Department of Molecular Biosciences in 2000, and became Foundation Executive Dean of the Faculty of Sciences in 2002, a role he kept until 2005. He was appointed Dean of the Faculty of Science at the University of Melbourne in 2006; in 2008, he became Dean of the GraduateSchool of Science, and from 2008 to 2011 he served as Deputy Vice-Chancellor. He was involved in Melbourne's controversial program of 'focused excellence', that shed some staff positions in order to reduce a growing debt. In April 2011 Rathjen took up the role of Vice-Chancellor at the University of Tasmania. During his vice-chancellorship, he promoted the University as a driver of socio-economic prosperity in Tasmania, including plans to move University of Tasmania campuses into CBD districts in Burnie, Launceston, and Hobart. During his vice-chancellorship, the university launched new associate degree programs. However, controversies during Rathjen's vice-chancellorship included the use of university funds for what was perceived as "travelling the globe in style", spending $50,000 in less than 6 months. In 2018, Rathjen returned to the University of Adelaide in the roles of Vice-Chancellor and President, in succession to Mike Brooks. In May 2020, Rathjen commenced an indefinite leave of absence after University of Adelaide Chancellor Kevin Scarce resigned without public explanation the previous day. Later in the week, the Independent Commissioner Against Corruption confirmed he was investigating allegations of improper conduct by the Vice-Chancellor of the University of Adelaide. Rathjen, accused of engaging in "a personal relationship with a staff member", was succeeded by Acting Vice-Chancellor Mike Brooks. Rathjen formally resigned in July 2020.
