Leaving Harwell in 1951 for the University of Liverpool he was Leverhulme Fellow and Lecturer (PhD 1957), beginning ten years of research on elementary particle physics, using newly developed proton synchrotron machines.
Senior physicist at CERN (the European Organization for Nuclear Research) from 1957 to 1960, subsequently Merrison was chair in experimental physics at Liverpool from 1960 until 1969.
In 1962 he was also first director of the new Daresbury Nuclear Physics Laboratory (officially opened in 1967), responsible for the construction of the 5 GeV electron synchrotron NINA.
In 1976 Merrison was appointed chair of the Royal Commission on the National Health Service (reporting in 1979) and though initially certain of its key recommendations were resisted, later a number formed the basis of NHS reform.
He received honorary degrees from a number of universities including Bristol, Bath and Liverpool and was appointed High Sheriff of Avon for 1986–1987.