Wilkinson's first academic position, from 1993 to 1997, was as
Lady Wallis Budge Research Fellow in Egyptology at
Christ's College, Cambridge. From 1997 to 1999, he was
Leverhulme Special Research Fellow at the
University of Durham. He set up the college's development office, focusing on communications, fundraising and external relations, and served as director of development from 2003 to 2010. He is a member of the editorial board of the
Journal of Egyptian History. He is an honorary research fellow in the Department of Archaeology, University of Durham. In July 2011, he became head of the International Strategy Office at the University of Cambridge. In this position, he developed the university's international strategy and helped facilitate international collaborations. In 2017, he became
Deputy Vice Chancellor (External Relations) at the
University of Lincoln. In January 2021, he moved to the South Pacific to become
Vice Chancellor of
Fiji National University. However, in August 2021, it was announced that he was to step down in December 2021 due to "personal family reasons", and he subsequently returned to the United Kingdom. In March 2022, it was announced that he would return to Clare College, Cambridge as Fellow for Development: he took up the appointment on 3 May 2022. He was appointed as the
bursar of Clare college in February 2025. ==Honours==