Professor Thomas, who has been Vice-Chancellor of the University of Bristol since September 2001, will hold the post for the next two academic years - 2011 to 2012 and 2012 to 2013.
He graduated in Medicine from the University of Newcastle upon Tyne in 1976 and, in 1991, was appointed Professor of Obstetrics and Gynaecology at the University of Southampton.
Professor Thomas became Head of the School of Medicine at Southampton and then was made Dean of the University’s Faculty of Medicine, Health and Biological Sciences in 1998.
Previous to his role as President of UUK, Professor Thomas was Vice-President as well as Chair of its England and Northern Ireland Council and Chair of its Research Policy Committee.
Professor Thomas said: “I am under no illusion that the road ahead will be a significantly challenging one for our sector. However, I am very keen that in amongst this, we do not lose sight of the immense strengths that our universities possess and the undoubted positive impact they bring to the UK economy, to society and to individuals.
“It is an honour and a privilege to have this opportunity to serve what is without doubt, one of the UK’s most important sectors globally.”