He studied at King's College, London and obtained a BSc degree in 1956 and PhD in 1960, for thesis research on the enzymology of transamination.
Ellis became scientific officer in the ARC (Agriculture Research Council) Unit of Plant Physiology, Imperial College, University of London, 1959–61 and an ARC Research Fellow at the Department of Biochemistry, University of Oxford, 1961–64, working on the regulation of bacterial sulphate reduction with Professor C. A. Pasternak.
In 1970, Ellis moved to the newly created Department of Biological Sciences, University of Warwick, as senior lecturer and founding head of the Chloroplast Research Group.
Ellis has remained at Warwick University as reader (1973), holder of a personal chair (1976), and emeritus professor (1996).
From 1990 until 2009, he organised annual meetings of the UK Molecular Chaperone Club at the Universities of Oxford, Cambridge, London, Bristol, Birmingham and Warwick.