Born in the United Kingdom, his father had previously won a PhD scholarship to Cambridge University. They moved to South Australia when he was a child where he had his schooling at Blackwood High School in Adelaide. He studied Science at the University of Adelaide, majoring in biochemistry and genetics, and completing an honours degree. He reached international standard at orienteering and was the reserve for the Australian team at the 1985 World Orienteering Championships.
He was awarded a Rhodes Scholarship to New College, Oxford where he continued research into certain plant pathogens called viroids and their association with RNA behaviour. This led to a post-doc at Oxford on embryonic stem cells.
Rathjen and his new wife Joy returned to South Australia, where he took a teaching role and in 1995 was appointed to the Chair of Biochemistry at the University of Adelaide, aged only 31. He became head of the new Department of Molecular Biosciences in 2000.
He became Foundation Executive Dean of the Faculty of Sciences at the University of Adelaide in 2002.
He was appointed Dean of the Faculty of Science at the University of Melbourne in 2006, but after two years was replaced by Prof. Liz Sonenberg and then Prof. Rob Saint, and became Deputy Vice-Chancellor (Research). He oversaw the foundation of nine interdisciplinary research institutes aimed at creating research synergies and funding in key areas, from broadband technology to sustainability and energy systems. He was also involved in Melbourne's controversial program of 'focussed excellence', that shed some staff positions and reduced a growing debt.
In April 2011 he took up the role of Vice-Chancellor at the University of Tasmania. Already known for strong support for academic excellence in the sciences, he immediately became embroiled in controversial remarks about the failures of Tasmania's school system. Rathjen also believes many university students cannot afford or cannot manage a standard Bachelor degree, and briefer and cheaper alternatives should be explored for them, relieving pressures on the standard university system.
His PhD work formed the foundations of gene shear technology which was commercialised by CSIRO. Further research involved the molecular genetics of yeast and the mechanism by which certain genes 'jumped out' of the DNA and reinserted themselves into other parts of the chromosome. In his final PhD year he worked on the same mechanism in mammalian DNA.
At Adelaide, Rathjen headed a research group looking at embryonic stem cells and protein signals which determine the final type of cells to be formed. This led to examination of commercial and therapeutic opportunities of the science.
He remains active in research, co-authoring 4 papers in 2010.
- Inaugural winner of the Premier of South Australia's Science Excellence Award in the category of Research Leadership.
- Founding member of the Australian Centre of Excellence for Biotechnology.
- Fellow, Australian Academy of Science (2001)
- Anger at uni boss's criticism. The Mercury, May 2, 2011. Retrieved on 2012-04-30.
- Mass university sector is unsustainable. ''The Australian'', May 4, 2011. Theaustralian.com.au (2012-02-17). Retrieved on 2012-04-30.
- Australian Academy of Science – Professor Peter Rathjen. Science.org.au (2009-04-07). Retrieved on 2012-04-30.
- PROF PETER RATHJEN. findanexpert.unimelb.edu.au
- "Prof Peter Rathjen". The University of Melbourne Voice. April–May 2006.
- "Professor Peter Rathjen Biochemist. Interview with Marian Heard". Australian Academy of Science. 2001.