After wartime work on the British and Canadian Atomic Energy projects, he returned to Cambridge in 1946, where he was awarded a PhD in 1947 and held posts culminating as Reader in Nuclear Physics from 1956–1957.  From 1944 to 1959, he was a fellow of Jesus College, Cambridge. 
In 1957 he went to the University of Oxford as Professor of Nuclear Physics.  In 1959 he became Professor of Experimental Physics at Oxford, and from 1962 to 1976 was head of the Department of Nuclear Physics.  While he held his professorship at Oxford, he was a Fellow (there called a Student) of Christ Church, Oxford.  He was knighted in 1974.  In 2001 the Nuclear Physics Laboratory at the University of Oxford, which he had helped to create, was renamed the Denys Wilkinson Building in his honour.
Denys Wilkinson's work in nuclear physics included investigation of the properties of nuclei with low numbers of nucleons.  He was amongst the first to experimentally test rules relating to isospin.  He also applied concepts from physics to the study of bird navigation. 
He died on 22 April 2016 at the age of 93. 
His papers are held at the Churchill Archives Centre in Cambridge.  He was an Honorary Fellow of Jesus College, Cambridge from 1961, and an Honorary Student of Christ Church, Oxford from 1979.  He won the Hughes Medal of the Royal Society in 1965 and the Royal Medal in 1980.    In 1980 he received an honorary doctorate from the Faculty of Mathematics and Science at Uppsala University, Sweden.
- His portrait (1990), by Keith Clements, held at the University of Sussex.
- "The Papers of Sir Denys Wilkinson". Janus. Cambridge University. Retrieved 2016-04-30.
- "Denys Wilkinson". The Royal Society. The Royal Society. Retrieved 2016-04-30.
- The London Gazette: . 13 December 1974. Retrieved 5 May 2009.
- Oxford Physics – Denys Wilkinson Building
- "University of Sussex's third Vice-Chancellor Sir Denys Wilkinson passes away on 22 April 2016". University of Sussex. University of Sussex. Retrieved 2016-04-30.
- "Award Winners [of Hughes Medal]". Royal Society. Retrieved 2016-04-30.
- "Award Winners [of Royal Medal]". Royal Society. Retrieved 2016-04-30.