| Honorific Prefix: | Sir |
| Honorific Suffix: | KCB |
| Jon Thompson | |
| Office: | Permanent Secretary at HM Revenue and Customs |
| Predecessor: | Dame Lin Homer |
| Successor: | Jim Harra |
| Term Start: | April 2016 |
| Term End: | October 2019 |
| Office2: | Permanent Secretary at the Ministry of Defence |
| Predecessor2: | Dame Ursula Brennan |
| Successor2: | Stephen Lovegrove |
| Term Start2: | July 2012 |
| Term End2: | April 2016 |
| Birth Date: | 29 December 1964 |
| Birth Place: | Norwich, Norfolk, England, UK |
| Nationality: | British |
| Occupation: | Civil servant |
Sir Jonathan Michael Thompson, (born 29 December 1964) is a British civil servant who served as the Permanent Secretary of the Ministry of Defence (MOD) from September 2012 until April 2016, when he succeeded Dame Lin Homer as Permanent Secretary and Chief Executive of HM Revenue and Customs. He became Chief Executive of the Financial Reporting Council after leaving HMRC in Autumn 2019.[1] [2]
Thompson was born in Norwich,[3] and educated at Earlham High School, Norwich City College and Anglia Polytechnic, which later became Anglia Ruskin University. He became CIPFA qualified in 1989.
Thompson was in local government as Finance Director for North Somerset Council.[4]
Thompson joined the Civil Service in 2004, as OFSTED’s first finance director. He moved to Department for Education and Skills as their Director-General for Corporate Services in 2006, leaving the then Department for Children, Schools and Families to join the Ministry of Defence (MOD) as Director General of Finance in 2009. Thompson became Permanent Secretary of the MOD in 2012 succeeding Ursula Brennan who moved to the Ministry of Justice. In 2015, he was paid a salary of between £165,000 and £169,999 by the MOD, making him one of the 328 most highly paid people in the British public sector at that time.[5] He then became Chief Executive and First Permanent Secretary of HM Revenue and Customs. Thompson is currently the Chief Executive of the Financial Reporting Council. Thompson is also a non-executive director on the board of HS2 Ltd.[6] In February 2023 he became chair of HS2 Ltd until, upon the resignation of CEO Mark Thurston in September 2023, Thompson took over the running of the company as executive chairman for an interim period.[7] [8] [9]
Thompson was appointed a Knight Commander of the Order of the Bath (KCB) in the 2019 New Year Honours, "for public service."
Thompson married his wife Dawn in 1987 and has three sons and one grandson and one granddaughter.[4] He is a supporter of Norwich City Football Club,[3] and lives in Cambridgeshire.[3]