In 1985 he returned to Australia and was appointed lecturer at The Australian National University. In 1988 Milburn took up an appointment as Reader in Theoretical Physics at The University of Queensland. In 1994 he was appointed as Professor of Physics and in 1996 became Head of Department of Physics at The University of Queensland. From 2000 to 2010 he was Deputy Director of the Australian Research Council Centre of Excellence for Quantum Computer Technology. From 2003 to 2013 he was an Australian Research Council Federation Fellow at the University of Queensland.
From 2011 to 2017 he was the Director and Chief Investigator of the Australian Research Council Centre of Excellence for Engineered Quantum Systems.[8]