He is a visiting professor of public health at the University of Bristol and is a member of the Independent SAGE group, formed during the COVID-19 pandemic in 2020.

After moving to England, he led several inquiries into serious NHS clinical failures including pathology in Swindon, breast screening in Exeter and abuse in Winterbourne.

Scally resigned as RDPH in 2012, and was appointed as an associate fellow at the Institute for Public Policy Research, and as a visiting professor at the University of Bristol and UWE.

[2] He attended St Mary's Christian Brothers Grammar School before gaining admission to study medicine at Queen's University Belfast.

[14] In light of the increasing number of public health personnel not trained in medicine, he advocated that they also be subject to statutory regulation.

[17] Subsequently, during Scally's position as RDPH in England, he became involved in a number of clinical failure inquiries, including pathology in Swindon, breast screening in Exeter and abuse in Winterbourne.

[31] They described the UK's response to the COVID-19 pandemic as "too little, too late, too flawed", with no adequate plan for community-based case-finding, testing, and contact tracing.

[5][37] In 2020 he expressed concerns about the management of the COVID-19 pandemic in Ireland in the newspaper Barron's,[38] the government's plans to end Public Health England (PHE),[39] and the implementation of Operation Moonshot.

[41] In 2002, he delivered the Royal College of Physicians' Milroy lecture, titled "The very pests of society’: the Irish and 150 years of public health in England", later published in Clinical Medicine.