An alumnus of the University of Edinburgh, graduating with MA Honours in Archaeology (1967), he became a lecturer there in 1974, was promoted to Reader in 1982 and was appointed Acting Head of Archaeology (1982–87).
From 1990–2004 he was Secretary of the Royal Commission on the Ancient and Historical Monuments of Scotland (RCAHMS). He retired in 2004 but retains ties with the University of Edinburgh's School of History, Classics and Archaeology where he is an Honorary Professorial Fellow.
Professor Mercer was awarded an OBE in January 2004 for services to Archaeology.
He has published widely on prehistoric Britain including:
- Farming Practice in British Prehistory, Edinburgh University Press, 1981
- Hambledon Hill: A Neolithic Landscape, Edinburgh University Press, 1980
- Staff page at the University of Edinburgh
- "Carn Brea, Early Neolithic tor enclosure, c 3700 BC". Royal Archaeology Society. Retrieved 4 January 2015.
- The Glasgow Herald, 18 August 1989, page 7