Jon Watson was born and educated in the UK. He attended Cambridge University for his undergraduate degrees in medicine (BA and MA in Medical Sciences), and Oxford University for his clinical studies (Bachelor of Medicine and Bachelor of Surgery). He trained as a physician and gastroenterologist in Oxford, London and Newcastle upon Tyne. Whilst working in Newcastle upon Tyne he was awarded a PhD for studies into Hepatitis C Virus infection and liver disease. He was awarded the European Certificate of Completion of Specialist Training (CCST) in 1998.
He then migrated to Australia, with his family. He has practised, researched and taught in Ballarat, Stawell, Newcastle, and Geelong. He is Professor of Medicine and Dean of the School of Medicine, Faculty of Health, Deakin University, Geelong.
He has clinical appointments at Epworth Geelong, Geelong Hospital, Geelong Private Hospital, St John of God Hospital (Geelong and Ballarat), Ballarat Day Procedure Centre, and Stawell Hospital.
He is a member of the National Examining Panel of the Royal Australasian College of Physicians, a Fellow of the Royal College of Physicians of London and a Fellow of the Royal Australasian College of Physicians.
He serves as a Board Director for both Kardinia Health Geelong, and the National Centre for Farmer Health in Hamilton, Victoria. In January 2016 he was appointed as National Board Chair for the Australasian College of Sports and Exercise Physicians.