Sir Jonathan qualified as a doctor at St Thomas' Hospital Medical School. In 1980 he was appointed Consultant Physician and Nephrologist at the Queen Elizabeth Hospital in Birmingham and Honorary Senior Lecturer at Birmingham University. He became a Fellow of the Royal College of Physicians (London) in 1985.
Sir Jonathan became increasingly involved in hospital management during the 1990s, being appointed Clinical Director, then Medical Director, and finally Chief Executive of the University Hospitals Birmingham NHS Trust. In 2000 he was recruited to the position of Chief Executive of Guy's and St Thomas' Hospitals NHS Trust in London, an organisation that he led to become one of the first wave of foundation trusts in the NHS.
He has held a number of regional and national roles, including membership of the UK Clinical Research Collaboration Board, Chairmanship of the Board of NHS Innovations (London), Chairmanship of the Association of UK University Hospitals and Chairmanship of the Board of the NHS Foundation Trust Network. Sir Jonathan was knighted in the New Year's Honours in 2005 for services to the NHS.
In 2007 Sir Jonathan was appointed by the Secretary of State for Health to chair an independent inquiry into the access to health care for children and adults with learning disabilities. The report, Healthcare for All, was published in July 2008.
After three years as Managing Director of BT Health, Sir Jonathan rejoined the NHS as Chief Executive of the Oxford Radcliffe Hospitals in April 2010 which became Oxford University Hospitals NHS Trust in November 2011.