[4] In 2008, she was seconded to the Department of Health to work with Lord Ara Darzi on the Next Stage Review of the NHS and was subsequently appointed Commander of the Order of the British Empire (CBE) for services to healthcare.

During her studies, Rafferty worked part-time as a nurse teacher and lecturer at the John Radcliffe Hospital and Open University.

Her research into the healthcare workforce was the first to establish the link between nurse staffing and patient mortality rates in the UK.

[4] Rafferty has worked clinically as a nurse at the Royal Infirmary of Edinburgh, the Queen's Medical Centre, Nottingham, and the John Radcliffe Hospital, Oxford.

[9] In 1991, she took up the position of lecturer and admissions tutor at the then newly established Department of Nursing and Midwifery studies at the University of Nottingham.

For the academic year 1994-1995 she was a Harkness Fellow at the University of Pennsylvania and subsequently took up the post of senior lecturer at the London School of Hygiene and Tropical Medicine where she established the Centre for Policy in Nursing Research.

Rafferty was promoted to Reader and became head of the Health Services Research Unit at the London School of Hygiene and Tropical Medicine in 2001.

[12] In 2018, it was announced that Rafferty would become the next President of the Royal College of Nursing (RCN), a position she held from January 2019 to July 2021.

She was inducted onto the Sigma Theta Tau International Hall of Fame in 2016 and in 2017 Rafferty was nominated as one of the 70 most influential nurses in the first 70 years of the National Health Service.